Статті в журналах з теми "Plant taxonomy; DNA barcoding; phylogenetic diversity"
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Aneva, Ina, Petar Zhelev, Georgi Bonchev, Irina Boycheva, Stiliana Simeonova, and Denitsa Kancheva. "DNA Barcoding Study of Representative Thymus Species in Bulgaria." Plants 11, no. 3 (January 20, 2022): 270. http://dx.doi.org/10.3390/plants11030270.
Повний текст джерелаАнотація:
We present a study on the taxonomy of eleven Thymus species, belonging to two sections and occurring naturally in Bulgaria. Four DNA barcoding markers—matK, rbcL, trnH-psbA and ITS—were applied to discriminate the species and to reveal their phylogenetic relationships. The results showed that rbcL has the lowest discriminating power regarding the studied species, while the other markers yielded results fitting better to the existing taxonomic schemes based on morphological traits. However, even in the case of better performing markers, the results were not straightforward—morphologically distinct species belonging to different sections were grouped together, and closely related species appeared genetically distinct. The results are typical for taxonomically complex groups, such as the genus Thymus, characterized in Bulgaria with great diversity, high percentage of endemism and still requiring a full and comprehensive taxonomic study. The results are discussed in the light of unresolved taxonomic problems and application of DNA barcoding methods.
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Nikitina, E. V., N. Yu. Beshko, and S. A. Omarov. "Assessment of plant species diversity (Lamiaceae Lindle.) in Uzbekistan based on DNA barcoding." IOP Conference Series: Earth and Environmental Science 1068, no. 1 (July 1, 2022): 012042. http://dx.doi.org/10.1088/1755-1315/1068/1/012042.
Повний текст джерелаАнотація:
Abstract Biological diversity preservation is important concept in modern science and environmental policy of Uzbekistan, improving the status of global biodiversity. Flora of Uzbekistan accounts over 4380 species of vascular plants. 378 taxa representing approximately 9% of currently recognized species diversity of Uzbekistan are considered as a national endemics. The present study aimed at species identification and inventory of wild, rare and endangered plant species based on molecular genetic techniques. For effective species identification and high results reliability, the genotyping of three-four loci of the combinations nuclear and chloroplast DNA-barcodes was performed for all studied species. The genotyping of marker sequences ITS, rbcL, trnL-trnF, matK for Dracocephalum adylovii I.I. Malzev is conducted the first time in Uzbekistan. The reliable similarity in the BLAST database is determined at the genus taxonomic level. 78 consensus nucleotide sequences were obtained for Lamiaceae species. The results of molecular phylogenetic analysis based on marker sequence encoding the matK fragment are presented for representative of three subfamilies: Lamioideae, Nepetoideae, Scutellarioideae recorded in the flora of Uzbekistan. Currently, the solution of biological diversity preservation is global. The possibility of successful application of DNA-barcoding for ecological monitoring is demonstrated.
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Ariyanti, Yanti, Ika Rini, Indah Oktaviani, and Sovia Leksikowati. "DNA Barcoding for Selected Mangrove-Based Estuary Fishes from Way Kambas National Park, Lampung Province, Indonesia." Journal of Tropical Life Science 11, no. 2 (May 31, 2021): 151–60. http://dx.doi.org/10.11594/jtls.11.02.04.
Повний текст джерелаАнотація:
Over the past decade, DNA barcoding has provided new insight into fish ecology and biosystematics and led to new species' discovery. DNA barcoding is a method for the recognition and identification of species using short, standardised DNA fragments. The correct taxonomic identification of species is critical for the assessment and monitoring of biodiversity. This study applied DNA barcoding techniques to identify selected fish species from a mangrove-based estuary in Way Kambas National Park, Lampung Province, Indonesia. The gene encoding cytochrome c oxidase subunit I (COI) was amplified and bi-directionally sequenced from 22 specimens. The resulting 680 base pairs (bp) sequence was used to identify species, obtain phylogenetic information, and analyse genetic distances. A neighbour-joining tree was constructed based on the mitochondrial COI gene using the Kimura two-parameter model. This study also exhibits conservation status for those identified species. Our findings will facilitate future studies of fish species diversity in mangrove estuary-based ecosystems and provide preliminary data in policymaking in conservation areas such as National Park.
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Sonexay, Rasphone, Thanh Dang Long, Thi Hoang Ho Nhi, Quang Nguyen Co, and Thi Hong Truong Hai. "Phylogenetic analysis of black piper (Piper spp.) population collected in different locations of Viet Nam based on the ITSU1-4 gene region." Research Journal of Biotechnology 17, no. 7 (June 25, 2022): 1–9. http://dx.doi.org/10.25303/1707rjbt001009.
Повний текст джерелаАнотація:
The internal transcribed spacer (ITS) of nuclear ribosomal DNA is one of the most commonly used DNA markers in plant phylogenetic and DNA barcoding analyses and it has been recommended as a core plant DNA barcode. To compare and find out the genetic diversity difference, some individuals Peper were collected in different localities in Vietnam when using the ITS of nuclear ribosomal DNA. The ITS gene region from the nuclear genomes was tested for suitability as DNA barcoding regions of thirty-nine Peper individuals. Universal primers were used and sequenced products were analyzed using the Maximum Likelihood method and Tamura-Nei model in the MEGA X program. We did not observe high variability in intraspecific distance within the ITSu1-4 gene region between individuals ranging from 0.000 to 0.155. The size of the gene region has fluctuated from 667 to 685 bp between different individuals with the percentage (G + C) contained in the ITSu1-4 gene region which ranged from 54.776% to 60.805%, mean = 60.174%. The values of Fu’s Fs, D, Fu and Li’s D* and F* were negative as well (Fs = -0.209, D = -1.824; p < 0.05, D* = -1.205; not significant, p > 0.10 and F* = -1.699; not significant, 0.10 > p > 0.05) indicating an excess of recently derived haplotypes and suggesting that either population expansion or background selection has occurred. The value of Strobeck’s S is high (S = 0.684). The results of evolutionary relationships of taxa obtained 3 groups with the highest value of Fst are shown in the pairs of groups II and III (Fst = 0.151) and the lowest is in groups II and I (Fst = 0.015). All of the new sequences have been deposited in GeneBank under the following accession numbers MZ636718 to MZ636756. This database is an important resource for researchers working on Species of Peper in Vietnam and also provides a tool to create ITSu1-4 databases for any given taxonomy.
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Palomares-Rius, Juan Emilio, Antonio Archidona-Yuste, Ilenia Clavero-Camacho, José A. Carreira de la Fuente, Ana Rey, Benjamín Viñegla, Gracia Liébanas, Carolina Cantalapiedra-Navarrete, and Pablo Castillo. "DNA Barcoding and Morphometry Reveal Further Cryptic Bio-Diversity within the Pin Nematode Genus Paratylenchus (Nematoda: Tylenchulidae)." Plants 11, no. 23 (December 5, 2022): 3385. http://dx.doi.org/10.3390/plants11233385.
Повний текст джерелаАнотація:
Paratylenchus species are obligate ectoparasitic nematodes on cultivated and wild herbaceous and woody plants occupying numerous soil categories. Several species may cause damage to several crops (viz. P. dianthus, P. enigmaticus, P. microdorus, P. hamatus and P. epacris on carnation, lettuce, rose and walnut, respectively). This investigation proves and emphasizes the relevance of applying integrative taxonomy for the accurate detection of Paratylenchus species in mountainous wild environments in the Malaga province, Southern Spain. This research analyzed 45 soil samples of maritimus pine and one of green heather in southern Spain and identified fourteen Paratylenchus species, two of them are described herein as new species (P. paraaonli sp. nov., P. plesiostraeleni sp. nov.), six of them were first reports for Spain (P. canchicus, P. nainianus, P. neonanus, P. salubris, Paratylenchus sp. 2 SAS, and P. wuae), and six species (P. caravaquenus, P. microdorus, P. nanus, P. neoamblycephalus, P. sheri, and P. variabilis) have been already reported in Spain. Accordingly, these data increase the biodiversity of pin nematodes in Spain comprising a total of 47 species (33.1% out of 142 total species of this genus). Phylogenetic analyses based on ribosomal and mitochondrial markers (D2-D3, ITS, and partial COI) resulted in a consistent position for the newly described Paratylenchus species in this study (P. plesiostraeleni sp. nov., P. paraaonli sp. nov.). Paratylenchus plesiostraeleni sp. nov. grouped in a separated subclade as unequivocal species from the P. straeleni-complex species (including P. straeleni and P. parastraeleni), and P. paraaonli sp. nov. clustered with P. vitecus, but clearly separate from this species. This study indicates that Paratylenchus species diversity in natural environments may be higher than expected, and this study may help in accurate identifications.
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El-Esawi, Mohamed A., Mohamed M. A. Elashtokhy, Sahar A. M. Shamseldin, Enas M. El-Ballat, Ehab M. Zayed, and Yasmin M. Heikal. "Analysis of Genetic Diversity and Phylogenetic Relationships of Wheat (Triticum aestivum L.) Genotypes Using Phenological, Molecular and DNA Barcoding Markers." Genes 14, no. 1 (December 22, 2022): 34. http://dx.doi.org/10.3390/genes14010034.
Повний текст джерелаАнотація:
Wheat (Triticum aestivum L.) is a key food crop, accounting for approximately 765 million tons produced worldwide. The present study evaluated 16 wheat genotypes using 19 morphological and phenological traits, 16 molecular markers (Inter Simple Sequence Repeats and Start Codon Targeted; ISSR and SCoT) and rbcL and matK plastid gene barcoding. The 16 wheat genotypes showed significant genetic variation using the markers assayed. Cell plot of phenological parameters revealed significant differences among the 16-day-old seedlings of wheat genotypes at Z1.1 growth stage. Collectively, W2 genotype had the lowest shoot length (SL), length of first internodes (LFI) and leaf area (LA) values, while W8 genotype had the highest diameter of first internode (DFI) and LA values. Furthermore, W7 genotype had the maximum plant biomass (PB) and leaf width (LW) values. Geometric models grouped wheat kernels into “rounded” and “nearly elongated”. Estimates of heritability (H2) for these morphological characters ranged from 4.93 to 100%. The highest H2 values were recorded for root number (RN) (100%) followed by SL (88.72%), LFI (88.30%), LA (87.76%) and Feret diameter (86.68%), while the lowest H2 value was recorded for DFI (4.93%). Furthermore, highly significant genotypic and phenotypic correlations were also observed among those traits. Reproducible fingerprinting profiles and high levels of polymorphism (PPB%) of SCoT (95.46%) and ISSR (82.41%) were recorded, indicating that they are effective tools for detecting genetic variation levels among wheat genotypes. The informativeness of markers were measured through estimation of polymorphic information content (PIC), resolving power (RP) and marker index (MI). The RP and PPB% of SCoT were significantly higher compared to those of ISSR. Comparatively, the two molecular markers were effective for studying genetic diversity among wheat genotypes, but SCoT markers were more informative. Moreover, based on the two chloroplast DNA regions (rbcL and matK), MatK was found to be more reliable for differentiating among T. aestivum genotypes. Taken together, using all the studied attributes, a clear taxonomic relationship can be used to identify T. aestivum species and improve their pragmatic production and development.
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Hasan, Ariba, Pirzada Jamal Ahmed Siddiqui, Shabir Ali Amir, and Jean-Dominique Durand. "DNA Barcoding of Mullets (Family Mugilidae) from Pakistan Reveals Surprisingly High Number of Unknown Candidate Species." Diversity 13, no. 6 (May 26, 2021): 232. http://dx.doi.org/10.3390/d13060232.
Повний текст джерелаАнотація:
The mullets are a widespread group of ecologically and economically important fishes of disputed taxonomy due to their uniform external morphology. Barcoding and phylogenetic studies from various locations around the world largely highlighted the species diversity underestimation using morphological criteria used to establish the taxonomy of the family. Here, we investigated the mullet species diversity from Pakistan, a biogeographic area where nearly no mullet species were genetically characterized. Morphological examination of 40 mullets reveals 6 known species (Planiliza macrolepis, P. klunzingeri, P. subviridis, Crenimugil seheli, Ellochelon vaigiensis, and Mugil cephalus). Using a references DNA barcode library, the DNA barcode-based species identification flagged eight molecular operational taxonomic units (MOTUs) belonging to five genera (Crenimugil, Ellochelon, Mugil, Osteomugil, and Planiliza). Among these MOTUs, only one was already present in Barcode of Life Data system, all other representing new Barcode Index Numbers (BIN). These results emphasize the importance of the recognition of cryptic species and the necessity to re-evaluate the overall diversity by the genetic characterization of different species of this family. DNA barcoding is an effective tool to reveal cryptic species that need to be considered in conservation and management measures of fisheries in Pakistan.
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Carneiro de Melo Moura, Carina, Fabian Brambach, Kevin Jair Hernandez Bado, Konstantin V. Krutovsky, Holger Kreft, Sri Sudarmiyati Tjitrosoedirdjo, Iskandar Z. Siregar, and Oliver Gailing. "Integrating DNA Barcoding and Traditional Taxonomy for the Identification of Dipterocarps in Remnant Lowland Forests of Sumatra." Plants 8, no. 11 (October 30, 2019): 461. http://dx.doi.org/10.3390/plants8110461.
Повний текст джерелаАнотація:
DNA barcoding has been used as a universal tool for phylogenetic inferences and diversity assessments, especially in poorly studied species and regions. The aim of this study was to contrast morphological taxonomy and DNA barcoding, using the three frequently used markers matK, rbcL, and trnL-F, to assess the efficiency of DNA barcoding in the identification of dipterocarps in Sumatra, Indonesia. The chloroplast gene matK was the most polymorphic among these three markers with an average interspecific genetic distance of 0.020. The results of the molecular data were mostly in agreement with the morphological identification for the clades of Anthoshorea, Hopea, Richetia, Parashorea, and Anisoptera, nonetheless these markers were inefficient to resolve the relationships within the Rubroshorea group. The maximum likelihood and Bayesian inference phylogenies identified Shorea as a paraphyletic genus, Anthoshorea appeared as sister to Hopea, and Richetia was sister to Parashorea. A better discriminatory power among dipterocarp species provided by matK and observed in our study suggests that this marker has a higher evolutionary rate than the other two markers tested. However, a combination of several different barcoding markers is essential for reliable identification of the species at a lower taxonomic level.
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Veldkornet, D. A., J. B. Adams, J. S. Boatwright, and A. Rajkaran. "Barcoding of estuarine macrophytes and phylogenetic diversity of estuaries along the South African coastline." Genome 62, no. 9 (September 2019): 585–95. http://dx.doi.org/10.1139/gen-2018-0067.
Повний текст джерелаАнотація:
Plant DNA barcoding serves as an effective approach to building community phylogenies and increasing our understanding of the factors that determine plant community assemblages. The aims of the study were to (i) barcode macrophytes with high estuarine fidelity and (ii) to determine the phylogenetic diversity (PD) of selected South African estuaries for conservation prioritisation. Three DNA barcoding gene regions (rbcLa, matK, and trnH-psbA) were assessed, and community phylogenies were constructed for 270 estuaries. Generally, the matK barcode had the greatest discrimination success rate of 67.4% (parsimony informative sites = 418). Closely related species formed clades that also represent estuarine habitat types. Estuaries with high phylogenetic diversity along the southeast coast were associated with a combination of mangrove and salt marsh habitats. Species richness was strongly and significantly correlated with PD (r = 0.93; p < 0.000). Based on mean pairwise distance (MPD), more temperate estuaries (56) showed significant phylogenetic clustering compared to subtropical estuaries (24) (p < 0.05). Similarly, based on mean nearest taxon distance (MNTD), significant phylogenetic clustering was highest in temperate estuaries (50) compared to subtropical estuaries (12) (p < 0.05). This suggests that the coexistence of plant species in estuaries is structured by both biotic and abiotic interactions.
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Farrington, Lachlan, Phyllis MacGillivray, Renate Faast, and Andrew Austin. "Investigating DNA barcoding options for the identification of Caladenia (Orchidaceae) species." Australian Journal of Botany 57, no. 4 (2009): 276. http://dx.doi.org/10.1071/bt08138.
Повний текст джерелаАнотація:
The application of molecular techniques for defining evolutionary units in Caladenia has largely focussed on addressing relationships at the subgeneric and deeper levels. However, in light of the morphological complexity present in this diverse genus, molecular markers offer additional characters for the refinement of taxonomy at the species level. In the present study, we explored the utility of marker systems with demonstrated application for defining fine-scale units, both in terms of phylogenetic information and in the context of DNA barcoding. We also provide a working example of the use of molecular techniques for identifying the source plants of pollinia collected from passively sampled pollinators and for identifying sterile plants.
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Liu, Liu, Ge, Huang, Zhou та Wan. "The Use of DNA Barcoding to Assess Phylogenetic β-Diversity in Mid-Subtropical Evergreen Broad-Leaved Forests of China". Forests 10, № 10 (20 жовтня 2019): 923. http://dx.doi.org/10.3390/f10100923.
Повний текст джерелаАнотація:
The application of quantifying phylogenetic information into measures of forest β-diversity is increasing for investigating the underlying drivers of community assembly along environmental gradients. In terms of assessing evolutionary inferences of community processes, a variety of plant DNA barcodes has been widely used in phylogenetic diversity measurements. However, relatively few studies have evaluated the effectiveness of DNA barcodes with using nuclear region in estimating phylogenetic β-diversity, particularly for communities in tropical or subtropical forests. In this study, we employed DNA barcodes combing with the nuclear region to construct the community phylogeny and examined the patterns of phylogenetic β-diversity of three mid-subtropical evergreen broad-leaved forests (EBLFs) in South China. Three phylogenetic construction methods were performed, including a Phylomatic-generated tree and two ML trees based on the combination of rbcL +matK +ITS with or without a constrained tree. Our results showed that the DNA barcodes including nuclear ITS constructed a highly resolved phylogenetic tree, but the application of a constrained tree had little influence on estimation of phylogenetic diversity metrics (mean pairwise distances and mean nearest taxon distances) based on branch lengths. Using both metrics and their standardized effect size metrics, we found that the patterns of phylogenetic β-diversity in mid-subtropical forests were non-random. There was a slight decline of phylogenetic β-diversity with increasing latitudes, but no trend was found along the altitude gradient. According to the analysis of variation partition, both environmental filtering and dispersion limitation could explain the variation of phylogenetic dissimilarity between communities in mid-subtropical EBLFs of China. Our results highlight the importance of neutrality and the niche conservatism in structuring the patterns of species diversity in subtropical woody communities.
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Steinke, Dirk, Miguel Vences, Walter Salzburger, and Axel Meyer. "TaxI: a software tool for DNA barcoding using distance methods." Philosophical Transactions of the Royal Society B: Biological Sciences 360, no. 1462 (September 8, 2005): 1975–80. http://dx.doi.org/10.1098/rstb.2005.1729.
Повний текст джерелаАнотація:
DNA barcoding is a promising approach to the diagnosis of biological diversity in which DNA sequences serve as the primary key for information retrieval. Most existing software for evolutionary analysis of DNA sequences was designed for phylogenetic analyses and, hence, those algorithms do not offer appropriate solutions for the rapid, but precise analyses needed for DNA barcoding, and are also unable to process the often large comparative datasets. We developed a flexible software tool for DNA taxonomy, named TaxI. This program calculates sequence divergences between a query sequence (taxon to be barcoded) and each sequence of a dataset of reference sequences defined by the user. Because the analysis is based on separate pairwise alignments this software is also able to work with sequences characterized by multiple insertions and deletions that are difficult to align in large sequence sets (i.e. thousands of sequences) by multiple alignment algorithms because of computational restrictions. Here, we demonstrate the utility of this approach with two datasets of fish larvae and juveniles from Lake Constance and juvenile land snails under different models of sequence evolution. Sets of ribosomal 16S rRNA sequences, characterized by multiple indels, performed as good as or better than cox1 sequence sets in assigning sequences to species, demonstrating the suitability of rRNA genes for DNA barcoding.
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Bryant, Peter, and Timothy Arehart. "Diversity and life-cycle analysis of Pacific Ocean zooplankton by video microscopy and DNA barcoding: Crustacea." Journal of Aquaculture and Marine Biology 10, no. 3 (July 26, 2021): 108–36. http://dx.doi.org/10.15406/jamb.2021.10.00314.
Повний текст джерелаАнотація:
Determining the DNA sequencing of a small element in the mitochondrial DNA (DNA barcoding) makes it possible to easily identify individuals of different larval stages of marine crustaceans without the need for laboratory rearing. It can also be used to construct taxonomic trees, although it is not yet clear to what extent this barcode-based taxonomy reflects more traditional morphological or molecular taxonomy. Collections of zooplankton were made using conventional plankton nets in Newport Bay and the Pacific Ocean near Newport Beach, California (Lat. 33.628342, Long. -117.927933) between May 2013 and January 2020, and individual crustacean specimens were documented by video microscopy. Adult crustaceans were collected from solid substrates in the same areas. Specimens were preserved in ethanol and sent to the Canadian Centre for DNA Barcoding at the University of Guelph, Ontario, Canada for sequencing of the COI DNA barcode. From 1042 specimens, 544 COI sequences were obtained falling into 199 Barcode Identification Numbers (BINs), of which 76 correspond to recognized species. For 15 species of decapods (Loxorhynchus grandis, Pelia tumida, Pugettia dalli, Metacarcinus anthonyi, Metacarcinus gracilis, Pachygrapsus crassipes, Pleuroncodes planipes, Lophopanopeus sp., Pinnixa franciscana, Pinnixa tubicola, Pagurus longicarpus, Petrolisthes cabrilloi, Portunus xantusii, Hemigrapsus oregonensis, Heptacarpus brevirostris), DNA barcoding allowed the matching of different life-cycle stages (zoea, megalops, adult). The results show the utility of DNA barcoding for matching life-cycle stages as well as for documenting the diversity of this group of organisms.
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RASOOL, Ajaz, Tariq AHMAD, Bashir Ahmad GANAI, and Shaziya GULL. "An overview of molecular identification of insect fauna with special emphasis on chalcid wasps (Hymenoptera: Chalcidoidea) of India." Acta agriculturae Slovenica 111, no. 1 (April 8, 2018): 229. http://dx.doi.org/10.14720/aas.2018.111.1.22.
Повний текст джерелаАнотація:
Identifying organisms has grown in importance as we monitor the biological effects of global climate change and attempt to preserve species diversity in the face of accelerating habitat destruction. Classical taxonomy falls short in this race to catalogue biological diversity before it disappears. Differentiating subtle anatomical differences between closely related species requires the subjective judgment of highly trained specialists – and few are being trained in institutes today. DNA barcodes allow non-experts to objectively identify species – from small, damaged, or even industrially processed material. The aim of DNA barcoding is to establish a shared community resource of DNA sequences commonly used for identification, discrimination or taxonomic classification of organisms. It is a method that uses a short genetic marker in an organism's DNA to identify and distinguish its belonging from particular species, varieties or inter varieties. This simple technique has attracted attention from taxonomists, ecologists, conservation biologists, agriculturists, plant-quarantine officers and studies using the DNA barcode has rapidly increased. The extreme diversity of insects and their economical, epidemiological and agricultural importance have made them a major target of DNA barcoding. In this review, we present an overview of DNA barcoding of insects with emphasis on Chalcid wasps of India.
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Chase, Mark W., Nicolas Salamin, Mike Wilkinson, James M. Dunwell, Rao Prasad Kesanakurthi, Nadia Haidar, and Vincent Savolainen. "Land plants and DNA barcodes: short-term and long-term goals." Philosophical Transactions of the Royal Society B: Biological Sciences 360, no. 1462 (September 12, 2005): 1889–95. http://dx.doi.org/10.1098/rstb.2005.1720.
Повний текст джерелаАнотація:
Land plants have had the reputation of being problematic for DNA barcoding for two general reasons: (i) the standard DNA regions used in algae, animals and fungi have exceedingly low levels of variability and (ii) the typically used land plant plastid phylogenetic markers (e.g. rbcL , trnL-F , etc.) appear to have too little variation. However, no one has assessed how well current phylogenetic resources might work in the context of identification (versus phylogeny reconstruction). In this paper, we make such an assessment, particularly with two of the markers commonly sequenced in land plant phylogenetic studies, plastid rbcL and internal transcribed spacers of the large subunits of nuclear ribosomal DNA (ITS), and find that both of these DNA regions perform well even though the data currently available in GenBank/EBI were not produced to be used as barcodes and BLAST searches are not an ideal tool for this purpose. These results bode well for the use of even more variable regions of plastid DNA (such as, for example, psbA-trnH ) as barcodes, once they have been widely sequenced. In the short term, efforts to bring land plant barcoding up to the standards being used now in other organisms should make swift progress. There are two categories of DNA barcode users, scientists in fields other than taxonomy and taxonomists. For the former, the use of mitochondrial and plastid DNA, the two most easily assessed genomes, is at least in the short term a useful tool that permits them to get on with their studies, which depend on knowing roughly which species or species groups they are dealing with, but these same DNA regions have important drawbacks for use in taxonomic studies (i.e. studies designed to elucidate species limits). For these purposes, DNA markers from uniparentally (usually maternally) inherited genomes can only provide half of the story required to improve taxonomic standards being used in DNA barcoding. In the long term, we will need to develop more sophisticated barcoding tools, which would be multiple, low-copy nuclear markers with sufficient genetic variability and PCR-reliability; these would permit the detection of hybrids and permit researchers to identify the ‘genetic gaps’ that are useful in assessing species limits.
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Qian, Zhi-Hao, Justus Mulinge Munywoki, Qing-Feng Wang, Itambo Malombe, Zhi-Zhong Li, and Jin-Ming Chen. "Molecular Identification of African Nymphaea Species (Water Lily) Based on ITS, trnT-trnF and rpl16." Plants 11, no. 18 (September 18, 2022): 2431. http://dx.doi.org/10.3390/plants11182431.
Повний текст джерелаАнотація:
The genus Nymphaea L. (water lily) is the most diverse genus in the family Nymphaeaceae, with more than 50 species worldwide, including 11 species distributed in Africa. The complex and variable morphology of Nymphaea makes it extremely difficult to accurately identify species based on morphological characteristics alone. DNA barcoding has the potential to identify species accurately. In this study, 158 Nymphaea populations from seven African countries were collected for species identification by ITS, trnT-trnF and rpl16. Additionally, the three candidate DNA barcodes were evaluated for genetic distance and barcoding gap. Based on the comprehensive analysis of sequence similarity, genetic distance method and phylogenetic tree, a total of 137 populations of seven Nymphaea species from African were well-identified, including N. lotus, N. petersiana, N. zenkeri, N. nouchali var. caerulea, N. micrantha and N. guineensis. ITS has more obvious advantages over trnT-trnF, rpl16 and trnT-trnF+rpl16 in the intraspecific and interspecific variation differences and barcoding gap and can identify most species. trnT-trnF and rpl16 can identify some species that cannot be identified by ITS. The results showed that it is more appropriate to apply the combination of ITS and trnT-trnF (or rpl16) as the DNA barcoding of Nymphaea. Additionally, this study further enriches the DNA barcoding database of Nymphaea and provides a reference basis for studying taxonomy, phylogenetics and evolutionary origin of Nymphaea.
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Szyp-Borowska, Iwona, and Katarzyna Sikora. "DNA barcoding: A practical tool for the taxonomy and species identification of entomofauna." Forest Research Papers 80, no. 3 (September 1, 2019): 227–32. http://dx.doi.org/10.2478/frp-2019-0021.
Повний текст джерелаАнотація:
AbstractDNA barcoding is an innovative system designed to provide rapid, accurate, and automatable species identification by using short, standardized gene regions as internal species codes. The mitochondrial cytochrome C oxidase I (COI) gene was proposed by Paul Hebert as an official marker for animals, because of its small intraspecific but large interspecific variation. Since the launch of the project Barcode of Life, this simple technique has caught the interest of taxonomists, ecologists and plant-quarantine officers charged with the control of pests and invasive species.The great diversity of insects and their importance have made this group a major target for DNA barcoding. In most cases, the identification of insect species by traditional methods based on morphological features requires specialist knowledge and is labor-intensive. DNA barcoding aims at meeting the challenge of monitoring and documenting the biodiversity of insects. The utility of DNA barcoding for identifying small insects, cryptic taxa or rare species, as well as many species of forest entomofauna that are impossible to discriminate morphologically throughout all of their life stages, is a subject discussed in this review. Due to its usefulness, also in Poland in the Forestry Research Institute, a method for identifying selected species of saproxylic beetles based on the sequence of the COI region was developed. In the future, this method will be used to assess the state of biodiversity and the naturalness of forest ecosystems. Therefore, this and other future implications of this promising new technique are also discussed here.
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-i-Abbas, Fakhar, Fakhar -i-Abbas, Fakhra Nazir, and Fida Muhammad Khan. "Molecular Taxonomy and Phylogenetic Analysis of Dove and Pigeon Species (Aves: Columbidae) of Pakistan, Based on COI Region of Mitochondrial DNA." Journal of Bioresource Management 7, no. 3 (September 10, 2020): 35–44. http://dx.doi.org/10.35691/jbm.0202.0138.
Повний текст джерелаАнотація:
Doves and Pigeons are the members of living family Columbidae (Order: Columbiformes) having a wide range of taxonomic diversity and geographic distribution. Seven species with one sample each of family Columbidae were collected via random sampling from different districts of Pakistan to carry out this study. The targeted gene region was sequenced and identified by using BLAST tool at National Center for Biotechnology Information (NCBI). CLUSTALW was used for sequence alignment and MEGA6 for reconstruction of phylogenetic trees to predict the effective ancestry of different Columbidae species. The following phylogenetic trees were obtained i.e. Maximum Likelihood tree, Neighborhood joining tree, Maximum parsimony tree and UPGMA tree. In the current study, COI gene barcoding and phylogenetic analysis of family Columbidae gave results of multiple alignment which showed that Columba livia livia and Columba eversmanni, closely resembled as well as Spilopelia senegalensis and Streptopelia decaocta. While Streptopelia tranquebarica and Spilopelia chinensis have great affinity due to small clade difference and Treron phoenicoptera was distinctly related to other species due to large clade difference.
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Du, Jianguo, Kar-Hoe Loh, Amy Yee-Hui Then, Xinqing Zheng, Teguh Peristiwady, Mohammed Rizman-Idid, and Man Alias. "First record of the dotted grouper Epinephelus epistictus (Temminck & Schlegel, 1843) (Perciformes, Serranidae) in Malaysia." ZooKeys 861 (July 8, 2019): 107–18. http://dx.doi.org/10.3897/zookeys.861.34043.
Повний текст джерелаАнотація:
Five specimens of Epinephelusepistictus (Temminck & Schlegel, 1843) were collected from a major landing site located on the west coast of Peninsula Malaysia during a fish faunal survey on 23 August 2017. The present study extends the distribution range of E.epistictus southwards from Andaman Sea to the Strait of Malacca. Species identification was confirmed by colour pattern and DNA barcoding (567 bp of cytochrome C oxidase I) of all E.epistictus specimens and nine closely related Epinephelus species. The interspecies genetic distance ranged from 0.002–0.245. This study also presents, for the first time for Malaysia, data on length-weight relationships and otolith measurements. It contributes to a better understanding of taxonomy, and phylogenetic and genetic diversity of E.epistictus.
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Réblová, Martina, Miroslav Kolařík, Jana Nekvindová, Kamila Réblová, František Sklenář, Andrew N. Miller, and Margarita Hernández-Restrepo. "Phylogenetic Reassessment, Taxonomy, and Biogeography of Codinaea and Similar Fungi." Journal of Fungi 7, no. 12 (December 20, 2021): 1097. http://dx.doi.org/10.3390/jof7121097.
Повний текст джерелаАнотація:
The genus Codinaea is a phialidic, dematiaceous hyphomycete known for its intriguing morphology and turbulent taxonomic history. This polyphasic study represents a new, comprehensive view on the taxonomy, systematics, and biogeography of Codinaea and its relatives. Phylogenetic analyses of three nuclear loci confirmed that Codinaea is polyphyletic. The generic concept was emended; it includes four morphotypes that contribute to its morphological complexity. Ancestral inference showed that the evolution of some traits is correlated and that these traits previously used to delimit taxa at the generic level occur in species that were shown to be congeneric. Five lineages of Codinaea-like fungi were recognized and introduced as new genera: Codinaeella, Nimesporella, Stilbochaeta, Tainosphaeriella, and Xyladelphia. Dual DNA barcoding facilitated identification at the species level. Codinaea and its segregates thrive on decaying plants, rarely occurring as endophytes or plant pathogens. Environmental ITS sequences indicate that they are common in bulk soil. The geographic distribution found using GlobalFungi database was consistent with known data. Most species are distributed in either the Holarctic realm or tropical geographic regions. The ancestral climatic zone was temperate, followed by transitions to the tropics; these fungi evolved primarily in Eurasia and Americas, with subsequent transitions to Africa and Australasia.
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Armenteros, Maickel, Ariadna Rojas-Corzo, Alexei Ruiz-Abierno, Sofie Derycke, Thierry Backeljau, and Wilfrida Decraemer. "Systematics and DNA barcoding of free-living marine nematodes with emphasis on tropical desmodorids using nuclear SSU rDNA and mitochondrial COI sequences." Nematology 16, no. 8 (2014): 979–89. http://dx.doi.org/10.1163/15685411-00002824.
Повний текст джерелаАнотація:
The diversity and phylogenetic relationships of the Desmodoridae, a widespread tropical family of free-living marine nematodes, is hitherto poorly known both from molecular and taxonomic points of view. We performed a molecular phylogenetic analysis of marine nematodes to: i) disentangle relationships among tropical desmodorid species; and ii) compare the performance of the nuclear SSU rDNA and mitochondrial COI nucleotide sequences in 42 and 45 nominal species, respectively, to identify species. We generated 27 new sequences of SSU rDNA belonging to five genera not previously sequenced, and 34 new sequences of COI belonging to six genera and four families not previously sequenced. The SSU rDNA tree confirmed the Enoplida to be a monophyletic sister group to the Chromadorida. The family Comesomatidae is a sister group of the Xyalidae within the Monhysterida. Both DNA markers confirmed the congruence between the morphology- and molecular-based phylogenetic inferences for most of the families. Desmodoridae was a monophyletic group, but the relationships within the family could not be recovered; the subfamilies Desmodorinae and Spiriniinae were not monophyletic meanwhile the monophyly of Stilbonematinae was not fully supported due to a few specimens of questionable identity. COI performed better than SSU rDNA to disentangle relationships among closely related species and suggested the presence of cryptic diversity within Desmodoridae. COI is effective to explore cryptic diversity and barcode species within Nematoda, with a possible threshold of genetic distance of 5% between conspecific and interspecific sequences, but DNA barcoding is limited by the poor knowledge of the diversity and taxonomy of the group and the lack of a good reference database of vouchered COI sequences.
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Aykut, Yilmaz. "The importance in DNA barcoding of the regions which is covering rRNA genes and its sequences in the genus Quercus L." Bangladesh Journal of Plant Taxonomy 27, no. 2 (December 11, 2020): 261–71. http://dx.doi.org/10.3329/bjpt.v27i2.50666.
Повний текст джерелаАнотація:
Turkey with 18 oak (Quercus) species is one of the richest country according to species number and diversity. The most important reason of the species diversity in Turkey is its location and geomorphological structure which increase climatic effects and seperate Turkey into different phytogeographic regions. Furthermore, hybridization behaviours which frequently observed between oak species, genetic drift, gene flow and ecological factors cause morphological variations in the plants species. All of these factors make it difficult to define the species concept for plant groups like oaks. Therefore, the region covering 18S rRNA gene/ ITS1/ 5.8S rRNA gene/ ITS2/ 25S rRNA gene and secondly intergenic spacer (IGS)/ 5S rRNA gene for barcoding were obtained from genbank and used as a useful tool for the determination and solution of the phylogenetic relations of taxonomically problematic species, also these barcoding regions were compared with each other according to species recognition ability for oak species. As a result, it can be stated that both barcoding regions have high variable sites based on sequence information to identify the species and evaluate relationships of species studied.
Bangladesh J. Plant Taxon. 27(2): 261-271, 2020 (December)
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ABDULLAH, MOHD LUTFI, SITI AZIZAH MOHD NOR, and DARLINA MD NAIM. "Use of DNA barcode in the identification of catfishes (Siluriformes: Ariidae) from Malaysia." Biodiversitas Journal of Biological Diversity 18, no. 4 (October 4, 2017): 1358–66. http://dx.doi.org/10.13057/biodiv/d180411.
Повний текст джерелаАнотація:
Abdullah ML, Nor SAM, Naim DMd. 2017. Use of DNA barcode in the identification of catfishes (Siluriformes: Ariidae) from Malaysia. Biodiversitas 18: 1358-1366. The genus Ariidae contains many valuable fish species threatened by overfishing, but knowledge on distribution and threats is still limited due to taxonomic ambiguities. The aim of this study was to apply DNA barcoding techniques to establish a resource of DNA for identification of Ariidae species in Malaysia. A 621 bp of mitochondrial cytochrome oxidase subunit I (COI) gene was utilized to resolve phylogenetic relationships and molecular taxonomy of eight presumed Malaysian Ariid species. We found the monophyly of most species was well established with a mean Kimura-2 parameter (K2P) interspecies distance of 9.6% except for two species, Arius venosus, and Nemapteryx caelata that have very low interspecies genetic distance. The BLAST result shows only two species matched the presumably eight identified fish species. Such discrepancies could arise as a result of misidentifications or errors in GenBank database input, hybridization or incomplete lineage sorting. We suggest the use of DNA barcoding is integrated into the workflow during taxonomic studies as it could significantly increase knowledge about species distributions.
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MacIvor, J. Scott. "DNA barcoding to identify leaf preference of leafcutting bees." Royal Society Open Science 3, no. 3 (March 2016): 150623. http://dx.doi.org/10.1098/rsos.150623.
Повний текст джерелаАнотація:
Leafcutting bees ( Megachile : Megachilidae) cut leaves from various trees, shrubs, wildflowers and grasses to partition and encase brood cells in hollow plant stems, decaying logs or in the ground. The identification of preferred plant species via morphological characters of the leaf fragments is challenging and direct observation of bees cutting leaves from certain plant species are difficult. As such, data are poor on leaf preference of leafcutting bees. In this study, I use DNA barcoding of the rcbL and ITS2 regions to identify and compare leaf preference of three Megachile bee species widespread in Toronto, Canada. Nests were opened and one leaf piece from one cell per nest of the native M. pugnata Say ( N =45 leaf pieces), and the introduced M. rotundata Fabricius ( N =64) and M. centuncularis (L.) ( N =65) were analysed. From 174 individual DNA sequences, 54 plant species were identified. Preference by M. rotundata was most diverse (36 leaf species, H ′=3.08, phylogenetic diversity ( pd )=2.97), followed by M. centuncularis (23 species, H ′=2.38, pd =1.51) then M. pugnata (18 species, H ′=1.87, pd =1.22). Cluster analysis revealed significant overlap in leaf choice of M. rotundata and M. centuncularis . There was no significant preference for native leaves, and only M. centuncularis showed preference for leaves of woody plants over perennials. Interestingly, antimicrobial properties were present in all but six plants collected; all these were exotic plants and none were collected by the native bee, M. pugnata . These missing details in interpreting what bees need offers valuable information for conservation by accounting for necessary (and potentially limiting) nesting materials.
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Pham, Thanh, Quynh Thi Nguyen, Duc Minh Tran, Hoi Nguyen, Hung Thai Le, Que Thi Hong Hoang, Yen Thi Van, and Thang Nam Tran. "Phylogenetic Analysis Based on DNA Barcoding and Genetic Diversity Assessment of Morinda officinalis How in Vietnam Inferred by Microsatellites." Genes 13, no. 11 (October 25, 2022): 1938. http://dx.doi.org/10.3390/genes13111938.
Повний текст джерелаАнотація:
Morinda officinalis How. is well-known as a valuable medicinal plant found in some regions of Vietnam. This species is mainly used for treating male impotence, irregular menstruation, and rheumatoid arthritis. This study aimed to identify the species of and genetic diversity in three M. officinalis populations: one each in Quang Binh (QB), Thua Thien Hue (TTH), and Quang Nam (QN). In this study, four DNA barcoding markers (ITS1, ITS2, matK, and rbcL) were used to identify the species and 22 microsatellite markers were applied for population structure and diversity analyses. The results showed that the sequences of gene regions studied in M. officinalis had a high similarity (>95%) to the ITS1, ITS2, matK, and rbcL sequences of M. officinalis on BLAST. Of the four DNA barcoding markers used, ITS1 and ITS2 showed higher efficiency in DNA amplification of M. officinalis. From this study, 27 GenBank codes were published on BLAST. The results also revealed high levels of genetic diversity in populations. The average observed and expected heterozygosity values were HO = 0.513 and HE = 0.612, respectively. The average FST value was 0.206. Analysis of molecular variance (AMOVA) showed 70% variation within populations and 30% among populations. The population structure of M. officinalis inferred in STRUCTURE revealed that the optimum number of genetic groups for the admixture model was K = 2. These findings provided vital background information for future studies in the conservation of M. officinalis in both ex situ and in situ plans.
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Ibrahim Khalil, Mohammed. "Molecular Identification and Phylogenetic Relationship of Some Plant Species In Ashdagh Mountain, Sangaw, Kurdistan Of Iraq." Academic Journal of Nawroz University 11, no. 4 (December 4, 2022): 400–404. http://dx.doi.org/10.25007/ajnu.v11n4a1194.
Повний текст джерелаАнотація:
Phylogenetic and molecular perspective of plant identification can reveal the plant composition of areas. Many new species have been identified based on morphological characters in different area of Kurdistan, but few have been identified through DNA barcoding method. In this study, Internal transcribed spacers 1 and 2 (ITS1 and ITS2) were used to identify some species in Ashdagh Mountain. The identified taxa were belonged to different families and clades and not recorded in any studies. The nucleotide sequences of identified species were 98-100% identical with species in the genebank database. The phylogenetic analysis showed diversity in phylogenetic relationships among coexisting species. In addition, the existing of Chara sp. in the acidic stream of Awa spi is a new record and not observed before. The finding of this study show the importance of using molecular and phylogenetic technique to identify and understand phylogenetic relationship among coexisting species because Kurdistan is a hot spot and need more emphasis. In addition, new species occurrence data has been added to flora of Kurdistan.
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Wardani, I. Gusti Ayu Kusuma, Fitri Yola Amandita, Carina Carneiro de Melo Moura, Oliver Gailing, and Iskandar Z. Siregar. "Molecular taxonomy via DNA barcodes for species identification in selected genera of Fabaceae." Jurnal Pengelolaan Sumberdaya Alam dan Lingkungan (Journal of Natural Resources and Environmental Management) 12, no. 1 (April 24, 2022): 112–22. http://dx.doi.org/10.29244/jpsl.12.1.112-122.
Повний текст джерелаАнотація:
Fabaceae is an invaluable plant family with considerable ecological and economic importances for example as food sources, bio-fertilizer, and medicinal plants. However, Fabaceae has been overexploited in Indonesia and several species belong to this family are critically endangered. Due to morphological similarity, rapid and accurate identification of Fabaceae species is essential to support its conservation efforts. Nowadays, species identification through DNA barcoding has become an effective taxonomic classification tool. This study was aimed to evaluate the effectiveness of chloroplast markers, matK and rbcL and the combination (matK+rbcL), as DNA barcodes for the identification of seleted genera in Fabaceae. The result showed that matK+rbcL and matK had the highest level of identification (90% and 82.05%) of the investigated genera, respectively. Additionally, matK had the highest mean of interspesific distance (0.134) and intraspecific distance (0.003). The combined barcode matK+rbcL had the highest correct identification rate when comparing the morphological with molecular identification. Furthermore, the best phylogenetic tree was obtained using Neighbor Joining method. Based on the overall performance, matK and matK+rbcL were the best barcodes for the selected genera in this study.
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PRIYONO, DWI SENDI, DEDY D. SOLIHIN, ACHMAD FARAJALLAH, and DIAH IRAWATI DWI ARINI. "Anoa, dwarf buffalo from Sulawesi, Indonesia: Identification based on DNA barcode." Biodiversitas Journal of Biological Diversity 19, no. 6 (October 9, 2018): 1985–92. http://dx.doi.org/10.13057/biodiv/d190602.
Повний текст джерелаАнотація:
Priyono DS, Solihin DD, Farajallah A, Arini DID. 2018. Anoa, dwarf buffalo from Sulawesi, Indonesia: Identification based on DNA barcode. Biodiversitas 19: 1985-1992. Anoa is an endangered endemic species in Sulawesi. The controversial issue of anoa conservation until now is the taxonomic status of lowland and mountain anoa. This study aims to test the ability of DNA barcoding techniques to identify the taxonomy between mountain anoa and lowland anoa. A 681bp fragment of cytochrome oxidase subunit 1 (COI) gene was obtained and used to solve the molecular taxonomic problem and to resolve the phylogenetic relationships of the two types of anoa. Our results showed that the DNA barcode is useful in assigning the taxonomic position of anoa. In the phylogenetic tree, we found that the two types of anoa were in separate clades. We also found that based on the Kimura-2 parameter (K2P), the genetic distance between the two types of anoa showed higher values (3.4%) than the threshold of the separating species level. We, therefore, proposed that the binomial nomenclature for both types of lowland and mountain anoa are respectively Bubalus depressicornis and Bubalus quarlesi. We suggest that the use of DNA barcode techniques in anoa taxonomic studies and their implementation will be useful in conservation management
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Zhang, Ying, Meizi Mo, Liu Yang, Fei Mi, Yang Cao, Chunli Liu, Xiaozhao Tang, Pengfei Wang, and Jianping Xu. "Exploring the Species Diversity of Edible Mushrooms in Yunnan, Southwestern China, by DNA Barcoding." Journal of Fungi 7, no. 4 (April 17, 2021): 310. http://dx.doi.org/10.3390/jof7040310.
Повний текст джерелаАнотація:
Yunnan Province, China, is famous for its abundant wild edible mushroom diversity and a rich source of the world’s wild mushroom trade markets. However, much remains unknown about the diversity of edible mushrooms, including the number of wild edible mushroom species and their distributions. In this study, we collected and analyzed 3585 mushroom samples from wild mushroom markets in 35 counties across Yunnan Province from 2010 to 2019. Among these samples, we successfully obtained the DNA barcode sequences from 2198 samples. Sequence comparisons revealed that these 2198 samples likely belonged to 159 known species in 56 different genera, 31 families, 11 orders, 2 classes, and 2 phyla. Significantly, 51.13% of these samples had sequence similarities to known species at lower than 97%, likely representing new taxa. Further phylogenetic analyses on several common mushroom groups including 1536 internal transcribed spacer (ITS) sequences suggested the existence of 20 new (cryptic) species in these groups. The extensive new and cryptic species diversity in wild mushroom markets in Yunnan calls for greater attention for the conservation and utilization of these resources. Our results on both the distinct barcode sequences and the distributions of these sequences should facilitate new mushroom species discovery and forensic authentication of high-valued mushrooms and contribute to the scientific inventory for the management of wild mushroom markets.
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Siriwut, Warut, Ekgachai Jeratthitikul, Somsak Panha, Ratmanee Chanabun, Peng Bun Ngor, and Chirasak Sutcharit. "Evidence of cryptic diversity in freshwater Macrobrachium prawns from Indochinese riverine systems revealed by DNA barcode, species delimitation and phylogenetic approaches." PLOS ONE 16, no. 6 (June 2, 2021): e0252546. http://dx.doi.org/10.1371/journal.pone.0252546.
Повний текст джерелаАнотація:
The diversity of Indochinese prawns in genus Macrobrachium is enormous due to the habitat diversification and broad tributary networks of two river basins: the Chao Phraya and the Mekong. Despite long-standing interest in SE-Asian decapod diversity, the subregional Macrobrachium fauna is still not yet comprehensively clarified in terms of taxonomic identification or genetic diversification. In this study, integrative taxonomic approaches including morphological examination, DNA barcoding, and molecular species delimitation were used to emphasize the broad scale systematics of Macrobrachium prawns in Indochina. Twenty-seven nominal species were successfully re-verified by traditional and molecular taxonomy. Barcode gap analysis supported broad overlapping of species boundaries. Taxonomic ambiguity of several deposited samples in the public database is related to inter- and intraspecific genetic divergence as indicated by BOLD discordance. Diagnostic nucleotide positions were found in six Macrobrachium species. Eighteen additional putative lineages are herein assigned using the consensus of species delimitation methods. Genetic divergence indicates the possible existence of cryptic species in four morphologically complex and wide-ranging species: M. lanchesteri, M. niphanae, M. sintangense, and some members of the M. pilimanus group. The geographical distribution of some species supports the connections and barriers attributed to paleo-historical events of SE-Asian rivers and land masses. Results of this study show explicitly the importance of freshwater ecosystems in Indochinese subregions, especially for the Mekong River Basin due to its high genetic diversity and species composition found throughout its tributaries.
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Martins, Nuno Tavares, Carlos Frederico D. Gurgel, Tracey M. Spokes, and Valéria Cassano. "species from south and south-eastern Australia (Ectocarpales, Phaeophyceae): a DNA barcoding approach." Australian Systematic Botany 34, no. 6 (October 14, 2021): 587–94. http://dx.doi.org/10.1071/sb21021.
Повний текст джерелаАнотація:
Defining species in the brown algal genus Colpomenia is a challenging endeavour because of their morphological similarity, overlapping phenotypic variation, the absence of conspicuous diagnostic characters, and often lack of reproductive structures crucial for their identification. Thus, the use of molecular tools has become widely used to study Colpomenia taxonomy and evolution. The following four Colpomenia species are described along the Australian coast: C. claytoniae M.Boo, K.M.Lee, G.Y.Cho & W.Nelson, C. ecuticulata M.J.Parsons, C. peregrina Sauvageau, and C. sinuosa (Mertens ex Roth) Derbès & Solier. The objective of this study was to assess the diversity of Colpomenia species in southern and south-eastern Australia by using DNA barcoding techniques and single-marker species delimitation methods. We generated 44 new COI-5P DNA sequences from nine different populations across three Australian states (South Australia, Victoria and Tasmania), and applied 13 variations of four species delimitation methods (ABDG, SPN, PTP, GMYC). Our results recognised three Colpomenia species in the region, namely, C. sinuosa, C. claytoniae, and C. peregrina. Colpomenia sinuosa is the most widely distributed species in Australia. Colpomenia peregrina and C. claytoniae presented high levels of intraspecific genetic divergence. We did not find C. ecuticulata, although it has been previously reported from nearby our sampling area.
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LYRA, GOIA DE MATTOS, JOSÉ MARCOS DE CASTRO NUNES, EDILENE MARIA DOS SANTOS PESTANA, JOÃO CARLOS GAMA DE MATOS, TAIARA AGUIAR CAIRES, PRISCILA BARRETO DE JESUS, EMMANUELLE DA SILVA COSTA, and MARIANA CABRAL OLIVEIRA. "DIVERSITY OF GRACILARIACEAE (RHODOPHYTA) IN BRAZIL: INTEGRATING MORPHOLOGICAL AND MOLECULAR DATA." Phytotaxa 496, no. 1 (April 9, 2021): 1–53. http://dx.doi.org/10.11646/phytotaxa.496.1.1.
Повний текст джерелаАнотація:
The Gracilariaceae comprises 242 mainly tropical species, including some with significant economic value for the food and pharmaceutical industry. Accurate taxonomy is crucial for the selection of species for cultivation. However, species identification is still challenging taxonomists. Nineteen species of Gracilariaceae have so far been referred to the Brazilian coast. We describe this diversity across approximately 32 degrees of latitude, using mitochondrial (COI-5P) and plastid (UPA and rbcL) markers in species delimitation analyses (ABGD and SPN). We provide phylogenetic (based on a concatenated three-genes tree and a taxa rich rbcL tree) and barcoding analyses from a broad and partially original collection combined with morphoanatomical data, including information resulting from analyses of type specimens and topotype material. We identified twenty-five specific entities occurring on the Brazilian coast, including four new species yet to be described. Spermatangial arrangements and aspects of thallus morphology were the most useful characters for species and genera delimitation, while characters based on the anatomy of the cystocarp overlap. Our morphological analyses demonstrate the lack of exclusive characters that justify the recently proposed Gracilariaceae infrafamilial categories, and therefore we use in this work the Gracilaria sensu lato genus concept. We provide descriptions, illustrations and a dichotomous key for the identification of species occurring in Brazil.
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NGUANHOM, JEERAPA, RATCHADAWAN CHEEWANGKOON, JOHANNES Z. GROENEWALD, UWE BRAUN, CHAIWAT TO-ANUN, and PEDRO W. CROUS. "Taxonomy and phylogeny of Cercospora spp. from Northern Thailand." Phytotaxa 233, no. 1 (October 30, 2015): 27. http://dx.doi.org/10.11646/phytotaxa.233.1.2.
Повний текст джерелаАнотація:
The genus Cercospora represents a group of important plant pathogenic fungi with a wide geographic distribution, being commonly associated with leaf spots on a broad range of plant hosts. The goal of the present study was to conduct a morphological and molecular phylogenetic analysis of the Cercospora spp. occurring on various plants growing in Northern Thailand, an area with a tropical savannah climate, and a rich diversity of vascular plants. Sixty Cercospora isolates were collected from 29 host species (representing 16 plant families). Partial nucleotide sequence data for two gene loci (ITS and cmdA), were generated for all isolates. Results from this study indicate that members of the genus Cercospora vary regarding host specificity, with some taxa having wide host ranges, and others being host-specific. Based on cultural, morphological and phylogenetic data, four new species of Cercospora could be identified: C. glycinicola (from Glycine max), C. cyperacearum and C. cyperina (from Cyperus alternifolius), and C. musigena (from Musa sp.). The most common Cercospora sp. found in Northern Thailand was C. cf. malloti, which occurred on a wide host range. Several collections could not be resolved to species level due to the lack of reference cultures and DNA data for morphologically similar species. Further collections from other countries are needed to help resolve the taxonomy of some species complexes occurring on various plant hosts in Thailand.
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Aissaoui, Chrifa, Nicolas Puillandre, Philippe Bouchet, Giulia Fassio, Maria Vittoria Modica, and Marco Oliverio. "Cryptic diversity in Mediterranean gastropods of the genus Aplus (Neogastropoda: Buccinidae)." Scientia Marina 80, no. 4 (November 22, 2016): 521. http://dx.doi.org/10.3989/scimar.04422.12a.
Повний текст джерелаАнотація:
Northeastern Atlantic and Mediterranean gastropods previously ascribed to the buccinid genus Pollia Gray, 1837 are more correctly classified in the genus Aplus de Gregorio, 1885. Using an integrative taxonomy approach combining molecular, morphological and geographic data, we revisit the limits of the extant species in the area, and propose a molecular phylogenetic hypothesis based on 66 specimens from various localities in the Mediterranean Sea, including type localities of some nominal taxa. We used a preliminary morphological inspection, followed by a DNA-barcoding approach to propose species hypotheses, subsequently consolidated using additional data (phylogenetic, geographic and refined morphological data). Seven species hypotheses were eventually retained within our molecularly assayed samples, versus three classical morphologically recognized species. Among these, three correspond to Aplus dorbignyi (Payreaudeau, 1826) with its hitherto unrecognized geographical cognates A. gaillardoti (Puton, 1856) (eastern Mediterranean) and Aplus nodulosus (Bivona Ant., 1832) (Sicily); two closely related, yet considerably divergent, lineages are treated as a single species under Aplus scaber (Locard, 1892); the classically admitted Aplus scacchianus (Philippi, 1844) is confirmed by molecular evidence; Mediterranean populations attributable to Aplus assimilis (Reeve, 1846) may represent either cryptic native populations or an ongoing invasion of the Mediterranean by what was hitherto considered to be a West African species; finally, specimens from the Strait of Gibraltar may represent an undescribed species, but we conservatively refrain from formally introducing it pending the analysis of more material, and it is compared with the similar Aplus campisii (Ardovini, 2014), recently described from Sicily and not assayed molecularly, and Aplus scaber.
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G, Anbarasi, and Vishnupriya B. "Molecular identification and phylogenetic analysis of suaeda maritima from parangipettai coastal areas, southeast coast of india." Kongunadu Research Journal 7, no. 1 (April 15, 2020): 28–34. http://dx.doi.org/10.26524/krj.2020.5.
Повний текст джерелаАнотація:
Conventional taxonomy is limited with delineating species and controversies arise with DNA barcoding based identifications. Hence, an alternative supporting approach is very much needed to identify species and differentiate them within the species based on the genetic material. 18S rRNA genes have been particularly helpful in analyzing phylogeny at the species level. In addition, bioinformatics which represents a new, growing area of science uses computational approaches to answer biological questions. Salt tolerant costal salt marsh plant of Suaeda maritima was selected for 18s rRNA sequencing to solve the ambiguity in itsspecies level identification. Similarity search of study species shared 99% similarity with 5 species of Atriplex canescens clone s128, Atriplex torreyi var. griffithsii clone p508, Spinacia oleracea, Oenothera laciniata clone,Beta vulgaris. Phylogenetic tree infer that S.maritima is closely related to Spinacia oleracea and Oenothera laciniata. Atriplex canescens (fourwing saltbush), Atriplex torreyi and Phaulothamnus spinescens, Celosia argentea found to be closely related and are in one group. Hence, this study result clearly shows thus study species evaluated from angiosperm and provides key step in understanding the evolution of salt tolerance in angiosperm.
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Nikitina, E., and Kh Khalbekova. "Species diversity and phylogenetic relationships within the tribe Mentheae (Lamiaceae) in Uzbekistan using ITS sequence data." IOP Conference Series: Earth and Environmental Science 1068, no. 1 (July 1, 2022): 012043. http://dx.doi.org/10.1088/1755-1315/1068/1/012043.
Повний текст джерелаАнотація:
Abstract Regular monitoring and comprehensive study of natural populations rare endangered species, both by classical taxonomy and molecular genetic analysis methods are of considerable importance all over the world. This work has focused at the research of species diversity flora of Uzbekistan using combinations of DNA markers. Currently, there are no universal DNA site for plant species identification. Pairwise sequence alignments and multiple sequence alignments are made using ClustalW program. DNA sequence data were used to verify the taxonomic identity and phylogenetic aspects of the studied representatives the tribe Mentheae (Lamiaceae) collected in Uzbekistan territory. The phylogenetic analyzes of this tribe was reconstructed for 44 species, representing 19 genera using nuclear ribosomal DNA internal transcribed spacer region (nrITS), containing ITS1 and ITS4 adopted as an important basis, since it can provide a high resolution of relationships. 15 consensus ITS gene sequences were obtained for studied species in this work and 29 published molecular sequence data from GenBank were used. Dendrograms were constructed using hierarchical clustering with the software Mega X. The parsimony analyses were resulted in an accurate consensus tree. Three major clades was identified within the tribe Mentheae. So, this paper demonstrates the successfully usefulness of DNA technology as a tool for genetic inventory at the species diversity assessment of rare endangered plants.
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Saunders, Gary W. "A DNA barcode examination of the red algal family Dumontiaceae in Canadian waters reveals substantial cryptic species diversity. 1. The foliose Dilsea–Neodilsea complex and WeeksiaThis paper is one of a selection of papers published in the Special Issue on Systematics Research." Botany 86, no. 7 (July 2008): 773–89. http://dx.doi.org/10.1139/b08-001.
Повний текст джерелаАнотація:
The field of DNA barcoding is working towards generating a genetic system for the quick and accurate identification of eukaryotic species. For the more systematic minded, however, DNA barcoding offers a new approach towards screening and uniting large numbers of biological specimens in genetic groups as a first step towards assigning them to species and genera in an approach best termed “molecular-assisted alpha taxonomy”. This approach is particularly amenable in organisms with simple morphologies, a propensity for convergence, extensive phenotypic plasticity, and life histories with an alternation of heteromorphic generations. It is hard to imagine a group of organisms better defined by all of these traits than the marine macroalgae. In an effort to assess the utility of the DNA barcode (COI-5′) for testing the current concepts of biodiversity of marine macroalgae in Canada, a study to assess species diversity in the red algal family, Dumontiaceae, was initiated. Through this work I confirm the presence in Canadian waters of Dilsea californica (J. Agardh) Kuntze, Dilsea integra (Kjellman) Rosenvinge, and Neodilsea borealis (I.A. Abbott) Lindstrom of the Dilsea–Neodilsea complex, and Weeksia coccinea (Harvey) Lindstrom for the genus Weeksia . However, our work has uncovered two additional species of the former complex, Dilsea lindstromiae Saunders sp. nov. and Dilsea pygmaea (Setchell) Setchell, and an additional species of the latter, Weeksia reticulata Setchell, effectively doubling representation of these foliose dumontiacean genera in Canadian waters.
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MAVRUK, SINAN, CIHAN TOSLAK, F. BANU YALIM, ARMAĞAN ERDEM ÜTÜK, ALPASLAN KARA, ÖZGÜR AKTAŞ, and AHSEN YÜKSEK. "First record of darter goby, Ctenogobius boleosoma (Jordan & Gilbert, 1882) (Gobiiformes: Gobiidae), in the Mediterranean with notes on larval morphology and cryptic diversity." Mediterranean Marine Science 23, no. 4 (October 24, 2022): 900–906. http://dx.doi.org/10.12681/mms.30161.
Повний текст джерелаАнотація:
Darter goby, Ctenogobius boleosoma (Jordan & Gilbert, 1882), is a small euryhaline fish of the Gobiidae family (Gobiiformes). It is naturally found in the shallow marine and brackish waters of the Western Central Atlantic. This study reports the first record of C. boleosoma in the Mediterranean Sea. In August and October 2019, two postflexion stage larvae were sampled during ichthyoplankton surveys in Antalya Bay in the Northeastern Mediterranean. The larvae were identified using the barcoding of cytochrome oxidase 1 gene sequence of mitochondrial DNA (COI). The morphology of the pre-transitional stage larvae was described and compared to previously published data. A phylogenetic analysis revealed that two distinct clades of C. boleosoma exist in its distribution range. The COI records belonging to one of the clades were generally collected within the Caribbean Sea, while the others were collected primarily in North American Western Atlantic waters from Florida to North Carolina. The average divergence between the clades was calculated to be 9.36 ± 1.34 (± 95% confidence interval), which likely indicates the existence of undescribed species. The specimen from the Mediterranean was identified as most closely related to the North American clade. This study shows how the integrative taxonomy of ichthyoplankton can improve knowledge about non-indigenous fish in the Mediterranean.
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GOU, WEI, XIAN-LIN GUO, SONG-DONG ZHOU, and XING-JIN HE. "Phylogeny and taxonomy of Meeboldia, Sinodielsia and their relatives (Apiaceae: Apioideae) inferred from nrDNA ITS, plastid DNA intron (rpl16 and rps16) sequences and morphological characters." Phytotaxa 482, no. 2 (January 29, 2021): 121–42. http://dx.doi.org/10.11646/phytotaxa.482.2.2.
Повний текст джерелаАнотація:
Meeboldia H.Wolff, Sinodielsia H.Wolff and their relatives (Apiaceae: Apioideae) are similar in morphology, of which taxonomic treatments were controversial. In this study, the nuclear ribosomal DNA sequence (ITS) and two plastid DNA markers (rps16 and rpl16) were applied to reconstruct phylogenetic trees. The results demonstrated that Meeboldia and Sinodielsia formed a monophyletic group in phylogenetic trees and their highly similar morphological characteristics in taproot, basal leaves, calyx teeth, ribs, and vittae of fruits also confirmed their close relationships. Consequently, the following results were obtained: (1) Sinodielsia should be merged into Meeboldia; (2) Sinodielsia delavayi was confirmed conspecific with Meeboldia yunnanensis and renamed as Meeboldia delavayi (Franch.) W.Gou & X.J.He; (3) Sinodielsia thibetica was away from other Sinodielsia species; (4) Sinodielsia microloba was a member of Meeboldia and renamed as Meeboldia microloba (Kljuykov) W.Gou & X.J.He; (5) The name of Sinodielsia clade was suggested to be replaced by Hymenidium clade. We applied multiple approaches to explore the relationship of morphologically similar taxa, which will facilitate a deep understanding of taxonomy and species diversity of Apiaceae.
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Marchán, Daniel Fernández, Thibaud Decaëns, Jorge Domínguez, and Marta Novo. "Perspectives in Earthworm Molecular Phylogeny: Recent Advances in Lumbricoidea and Standing Questions." Diversity 14, no. 1 (January 4, 2022): 30. http://dx.doi.org/10.3390/d14010030.
Повний текст джерелаАнотація:
Earthworm systematics have been limited by the small number of taxonomically informative morphological characters and high levels of homoplasy in this group. However, molecular phylogenetic techniques have yielded significant improvements in earthworm taxonomy in the last 15 years. Several different approaches based on the use of different molecular markers, sequencing techniques, and compromises between specimen/taxon coverage and phylogenetic information have recently emerged (DNA barcoding, multigene phylogenetics, mitochondrial genome analysis, transcriptome analysis, targeted enrichment methods, and reduced representation techniques), providing solutions to different evolutionary questions regarding European earthworms. Molecular phylogenetics have led to significant advances being made in Lumbricidae systematics, such as the redefinition or discovery of new genera (Galiciandrilus, Compostelandrilus, Vindoboscolex, Castellodrilus), delimitation and revision of previously existing genera (Kritodrilus, Eophila, Zophoscolex, Bimastos), and changes to the status of subspecific taxa (such as the Allolobophorachaetophora complex). These approaches have enabled the identification of problems that can be resolved by molecular phylogenetics, including the revision of Aporrectodea, Allolobophora, Helodrilus, and Dendrobaena, as well as the examination of small taxa such as Perelia, Eumenescolex, and Iberoscolex. Similar advances have been made with the family Hormogastridae, in which integrative systematics have contributed to the description of several new species, including the delimitation of (formerly) cryptic species. At the family level, integrative systematics have provided a new genus system that better reflects the diversity and biogeography of these earthworms, and phylogenetic comparative methods provide insight into earthworm macroevolution. Despite these achievements, further research should be performed on the Tyrrhenian cryptic complexes, which are of special eco-evolutionary interest. These examples highlight the potential value of applying molecular phylogenetic techniques to other earthworm families, which are very diverse and occupy different terrestrial habitats across the world. The systematic implementation of such approaches should be encouraged among the different expert groups worldwide, with emphasis on collaboration and cooperation.
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DARIENKO, TATYANA, and THOMAS PRÖSCHOLD. "The genus Jaagichlorella Reisigl (Trebouxiophyceae, Chlorophyta) and its close relatives: an evolutionary puzzle." Phytotaxa 388, no. 1 (January 14, 2019): 47. http://dx.doi.org/10.11646/phytotaxa.388.1.2.
Повний текст джерелаАнотація:
The genus Chlorella (in its traditional sense) is polyphyletic and belongs to at least twelve independent lineages of the Trebouxiophyceae and Chlorophyceae. Most of the aquatic species belong to the Chlorella and Parachlorella clades (within the so-called Chlorella-lineage of the Trebouxiophyceae), or to the genera Scenedesmus and Mychonastes (within the DO-group of the Chlorophyceae) according to phylogenetic analyses of the SSU and ITS rDNA sequences. In contrast to the aquatic species, the terrestrial strains investigated so far form a monophyletic lineage (Watanabea-clade) within the Trebouxia-lineage of the Trebouxiophyceae. Several genera with Chlorella-like morphology (Chloroidium, Heterochlorella, Watanabea, Kalinella, Viridiella and others) belong to the Watanabea clade. We studied 22 strains isolated from soil, bark, and artificial hard substrates, which have been traditionally identified as Chlorella luteoviridis or as unidentified Chlorella. To clarify the taxonomical status and intrageneric diversity of this group, we used an integrated approach (molecular phylogeny of SSU and ITS rDNA sequences, secondary structures, DNA barcoding, and morphology) including the ecological distribution. All investigated strains showed a low phenotypic plasticity, but a high genetic diversity, which could be only resolved in complex phylogenetic analyses based on the secondary structures of the investigated genes. Considering these results, we reestablished the genus Jaagichlorella for Heterochlorella and Heveochlorella, and proposed new combinations (J. luteoviridis, J. hainangensis, J. roystonensis, and J. sphaerica) as well as the new species, J. africana.
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FERREIRA, ELAINE CRISTINA BATISTA, MOISES THIAGO DE SOUZA FREITAS, KARLA DIANA DA SILVA SOMBRA, HERBERT ÁLVARO ABREU DE SIQUEIRA, ELTON LUCIO DE ARAUJO, and VALDIR DE QUEIROZ BALBINO. "MOLECULAR IDENTIFICATION OF Liriomyza sp. IN THE NORTHEAST AND SOUTHEAST REGIONS OF BRAZIL." Revista Caatinga 30, no. 4 (December 2017): 892–900. http://dx.doi.org/10.1590/1983-21252017v30n409rc.
Повний текст джерелаАнотація:
ABSTRACT In Brazil, species of the genus Liriomyza are widely distributed and have economic importance as they cause damage to at least 14 plant families, especially Solanaceae, Cucurbitaceae, Asteraceae, and Fabaceae. Studies suggest existence of a species complex within this genus, based on the presence of morphological similarities among the species Liriomyza trifolii (Burgess), L. sativae Blanchard and L. huidobrensis (Blanchard). The present study aimed to use DNA barcoding to establish new distribution records of L. sativae in distinct regions in Brazil, determine intra- and inter-population genetic diversity, and reconstruct the phylogeny of Liriomyza species using the DNA barcode sequences. Identity values were between 97% and 99%, confirming that all the examined Brazilian populations belonged to the species L. sativae. Phylogenetic analyses indicated the presence of a single clade of L. sativae, composed of seven populations. Intra-population analysis on individuals of these populations indicated low levels of nucleotide and haplotype diversity. The haplotype network indicated presence of only 14 haplotypes distributed among the Brazilian populations. The genetic similarities shared by the Brazilian populations of L. sativae suggest that these populations are closely related. Genetic patterns observed among populations of L. sativae might be associated with bottleneck events or founder effect during establishment of this leafminer in Brazil.
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Nundaeng, Supakorn, Nakarin Suwannarach, Savitree Limtong, Surapong Khuna, Jaturong Kumla, and Saisamorn Lumyong. "An Updated Global Species Diversity and Phylogeny in the Genus Wickerhamomyces with Addition of Two New Species from Thailand." Journal of Fungi 7, no. 11 (November 11, 2021): 957. http://dx.doi.org/10.3390/jof7110957.
Повний текст джерелаАнотація:
Ascomycetous yeast species in the genus Wickerhamomyces (Saccharomycetales, Wickerhamomycetaceae) are isolated from various habitats and distributed throughout the world. Prior to this study, 35 species had been validly published and accepted into this genus. Beneficially, Wickerhamomyces species have been used in a number of biotechnologically applications of environment, food, beverage industries, biofuel, medicine and agriculture. However, in some studies, Wickerhamomyces species have been identified as an opportunistic human pathogen. Through an overview of diversity, taxonomy and recently published literature, we have updated a brief review of Wickerhamomyces. Moreover, two new Wickerhamomyces species were isolated from the soil samples of Assam tea (Camellia sinensis var. assamica) that were collected from plantations in northern Thailand. Herein, we have identified these species as W. lannaensis and W. nanensis. The identification of these species was based on phenotypic (morphological, biochemical and physiological characteristics) and molecular analyses. Phylogenetic analyses of a combination of the internal transcribed spacer (ITS) region and the D1/D2 domains of the large subunit (LSU) of ribosomal DNA genes support that W. lannaensis and W. nanensis are distinct from other species within the genus Wickerhamomyces. A full description, illustrations and a phylogenetic tree showing the position of both new species have been provided. Accordingly, a new combination species, W. myanmarensis has been proposed based on the phylogenetic results. A new key for species identification is provided.
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Thinh, B. B., R. V. Doudkin, L. D. Chac, H. V. Chinh, Q. V. Hoi, and N. T. Lien. "Identification of Tinomiscium petiolare from Vietnam using the DNA barcode." Proceedings on applied botany, genetics and breeding 182, no. 2 (July 1, 2021): 114–22. http://dx.doi.org/10.30901/2227-8834-2021-2-114-122.
Повний текст джерелаАнотація:
Background. Tinomiscium petiolare Hook.f. & Thomson is a medicinal species of the family Menispermaceae. This species is currently being intensively exploited for therapeutic purposes. Precise and rapid identification of T. petiolare is critical and essential for the classification, propagation, use and conservation of its genetic resources. In recent years, DNA barcoding has been known to be a fast and sensitive method for identifying species at any stage of development, using short DNA sequences. In this study we have performed the identification of T. petiolare specimens in Vietnam based on the sequence analysis of 4 DNA barcode loci: ITS, matK, rbcL and rpoC.Materials and methods. Total DNA was extracted from leaf samples using DNeasy Plant Mini Kit. PCR amplification of the ITS, matK, rbcL and rpoC regions was carried out on the GeneAmp PCR System 9700 with specific primers. The purified PCR products were sequenced on the ABI 3500 Genetic Analyzer system, using BigDye®Terminator v3.1 Cycle Sequencing Kit. These genetic sequences were analyzed and compared, and a phylogenetic tree was constructed using BioEdit, BLAST, and MEGA 6 programs.Results and conclusion. The success rate of amplification and sequencing was 100% for all 4 DNA barcode loci (ITS, matK, rbcL and rpoC) in the studied specimens. The produced sequence sizes of ITS, matK, rbcL and rpoC in the specimens were 574 bp, 810 bp, 527 bp and 488 bp, respectively. Further, we identified that all studied specimens were genetically related to each other and associated with the same species T. petiolare. Overall, the results of the study generated the most complete DNA barcode database of T. petiolare collected in Vietnam, contributing to the taxonomy and identification of this species.
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Spjut, Richard, Antoine Simon, Martin Guissard, Nicolas Magain, and Emmanuël Sérusiaux. "The fruticose genera in the Ramalinaceae (Ascomycota, Lecanoromycetes): their diversity and evolutionary history." MycoKeys 73 (September 11, 2020): 1–68. http://dx.doi.org/10.3897/mycokeys.73.47287.
Повний текст джерелаАнотація:
We present phylogenetic analyses of the fruticose Ramalinaceae based on extensive collections from many parts of the world, with a special focus on the Vizcaíno deserts in north-western Mexico and the coastal desert in Namibia. We generate a four-locus DNA sequence dataset for accessions of Ramalina and two additional loci for Niebla and Vermilacinia. Four genera are strongly supported: the subcosmopolitan Ramalina, the new genus Namibialina endemic to SW Africa, and a duo formed by Niebla and Vermilacinia, endemic to the New World except the sorediate V. zebrina that disjunctly occurs in Namibia. The latter three genera are restricted to coastal desert and chaparral where vegetation depends on moisture from ocean fog. Ramalina is subcosmopolitan and much more diverse in its ecology. We show that Ramalina and its sister genus Namibialina diverged from each other at c. 48 Myrs, whereas Vermilacinia and Niebla split at c. 30 Myrs. The phylogeny of the fruticose genera remains unresolved to their ancestral crustose genera. Species delimitation within Namibialina and Ramalina is rather straightforward. The phylogeny and taxonomy of Vermilacinia are fully resolved, except for the two youngest clades of corticolous taxa, and support current taxonomy, including four new taxa described here. Secondary metabolite variation in Niebla generally coincides with major clades which are comprised of species complexes with still unresolved phylogenetic relationships. A micro-endemism pattern of allopatric species is strongly suspected for both genera, except for the corticolous taxa within Vermilacinia. Both Niebla and saxicolous Vermilacinia have chemotypes unique to species clades that are largely endemic to the Vizcaíno deserts. The following new taxa are described: Namibialinagen. nov. with N. melanothrix (comb. nov.) as type species, a single new species of Ramalina (R. krogiae) and four new species of Vermilacinia (V. breviloba, V. lacunosa, V. pustulata and V. reticulata). The new combination V. granulans is introduced. Two epithets are re-introduced for European Ramalina species: R. crispans (= R. peruviana auct. eur.) and R. rosacea (= R. bourgeana auct. p.p). A lectotype is designated for Vermilacinia procera. A key to saxicolous species of Vermilacinia is presented.
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Sathyanarayana, N., S. Mahesh, M. Leelambika, M. Jaheer, R. Chopra, and K. V. Rashmi. "Role of genetic resources and molecular markers inMucuna pruriens(L.) DC improvement." Plant Genetic Resources 14, no. 4 (March 28, 2016): 270–82. http://dx.doi.org/10.1017/s1479262116000071.
Повний текст джерелаАнотація:
AbstractMucuna pruriens(L.) DC is a tropical legume cover crop with promising nutritional and agronomic potentials. It is also a key source of 3,4 dihydroxy-L-phenylalanine (L-Dopa) – a precursor of dopamine used in the treatment of Parkinson's disease. However, lack of well-characterized germplasm plus poor accessibility to genomic resources has hindered its breeding programs. Furthermore, the cause and effect of various biotic and abiotic stresses impacting yield is also little studied. Systematic collection and evaluation of Indian germplasm by our group revealed presence of a diverse gene pool in India that can support a variety of breeding needs. The stability of L-Dopa trait across environments examined through Genotype and environment (G × E) interaction studies, as well as feasibility check on barcoding and phylogenetic analyses based on karyotype and conserved nuclear and chloroplast genes showed promising outcome. Germplasm screening for select biotic abiotic stresses identified resilient genotypes. Advances in use of DNA markers for diversity analysis, linkage map development, tagging of genes/quantitative trait loci for qualitative and quantitative traits, and progress in genomics are presented.
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Breitling, Rainer. "A BARCODE-BASED PHYLOGENETIC SCAFFOLD FOR XYSTICUS AND ITS RELATIVES (ARANEAE: THOMISIDAE: CORIARACHNINI)." Ecologica Montenegrina 20 (March 27, 2019): 198–206. http://dx.doi.org/10.37828/em.2019.20.16.
Повний текст джерелаАнотація:
The phylogenetic relationships and taxonomy of the crab spider genus Xysticus and its closest relatives (i.e., the tribe Coriarachnini, also including, e.g., Ozyptila, Coriarachne and Bassaniana) have long been controversial, with several alternative classifications being proposed, none of which has gained universal acceptance. As Coriarachnini is largely confined to the Holarctic region, the main target area of recent DNA barcoding projects for spiders, a large amount of genetic data for the group is now publicly available. The results of a phylogenetic analysis of this sequence dataset are largely congruent with earlier morphology-based results regarding the evolutionary structure of the group. In particular, they highlight the fact that Xysticus s. lat. is a paraphyletic assembly and that several species groups need to be placed in separate genera to achieve monophyly of Xysticus s. str. Similarly, Coriarachne and Bassaniana appear as independent clades rather than a joined monophyletic Coriarachne s. lat. In contrast, further subdivision of Ozyptila is not supported by the genetic data. Importantly, the analysis also shows that anapophysate members of Xysticus s. lat. form two widely separated groups: a primarily anapophysate division, also including Coriarachne and Bassaniana, at the base of Xysticus s. lat., and a secondarily anapophysate clade deeply nested within Xysticus s. str. This might explain some of the earlier difficulties when trying to define generally accepted subgroups within Xysticus s. lat. The phylogenetic scaffold based on barcode sequences is sufficiently dense and well resolved to attempt the tentative and provisional placement of the majority of species in Xysticus s. lat. in the independent genera Xysticus s. str., Bassaniodes, Psammitis and Spiracme as a starting point for a future more formal revision of the group.
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Thitla, Tanapol, Jaturong Kumla, Surapong Khuna, Saisamorn Lumyong, and Nakarin Suwannarach. "Species Diversity, Distribution, and Phylogeny of Exophiala with the Addition of Four New Species from Thailand." Journal of Fungi 8, no. 8 (July 24, 2022): 766. http://dx.doi.org/10.3390/jof8080766.
Повний текст джерелаАнотація:
The genus Exophiala is an anamorphic ascomycete fungus in the family Herpotrichiellaceae of the order Chaetothyriales. Exophiala species have been classified as polymorphic black yeast-like fungi. Prior to this study, 63 species had been validated, published, and accepted into this genus. Exophiala species are known to be distributed worldwide and have been isolated in various habitats around the world. Several Exophiala species have been identified as potential agents of human and animal mycoses. However, in some studies, Exophiala species have been used in agriculture and biotechnological applications. Here, we provide a brief review of the diversity, distribution, and taxonomy of Exophiala through an overview of the recently published literature. Moreover, four new Exophiala species were isolated from rocks that were collected from natural forests located in northern Thailand. Herein, we introduce these species as E. lamphunensis, E. lapidea, E. saxicola, and E. siamensis. The identification of these species was based on a combination of morphological characteristics and molecular analyses. Multi-gene phylogenetic analyses of a combination of the internal transcribed spacer (ITS) and small subunit (nrSSU) of ribosomal DNA, along with the translation elongation factor (tef), partial β-tubulin (tub), and actin (act) genes support that these four new species are distinct from previously known species of Exophiala. A full description, illustrations, and a phylogenetic tree showing the position of four new species are provided.
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Randrianiaina, Roger-Daniel, Axel Strauß, Julian Glos, Frank Glaw, and Miguel Vences. "Diversity, external morphology and ‘reverse taxonomy’ in the specialized tadpoles of Malagasy river bank frogs of the subgenus Ochthomantis (genus Mantidactylus)." Contributions to Zoology 80, no. 1 (February 11, 2011): 17—S11. http://dx.doi.org/10.1163/18759866-08001002.
Повний текст джерелаАнотація:
We provide detailed morphological descriptions of the tadpoles of Malagasy river bank frogs of the subgenera Ochthomantis and Maitsomantis (genus Mantidactylus, family Mantellidae), and data on relative abundance and habitat preferences of Ochthomantis species from Ranomafana National Park in southeastern Madagascar. Our study includes the tadpoles of six described and four undescribed candidate species. Eight of these larvae were previously unknown. Tadpoles were identified by DNA barcoding. Due to the very rudimentary taxonomic knowledge on Ochthomantis, we followed a ‘reverse taxonomy’ approach in which adult classification was to a great part determined on the basis of larval differences. By this procedure we even identified one candidate species whose adults remain still unknown. The majority of tadpoles in Ochthomantis and Maitsomantis have a rather similar body shape and they usually have similar habitat requirements. However, on the basis of the structure of their oral disk we identified three distinct groups: the first includes the femoralis-like tadpoles of Mantidactylus femoralis, M. ambreensis, M. zolitschka, M. argenteus, and of the candidate species named M. sp. 42, M. sp. 43 and M. sp. 47. They all have a reduced oral disk with poorly keratinized jaw sheaths and labial teeth. The mocquardi-like tadpoles of M. mocquardi and M. sp. 64 are placed in the second group and are characterized by a further reduction of oral disk structures, i.e. a complete lack of labial teeth. The third group includes only M. majori and is characterized by the transformation of the upper jaw sheath into three thorn-shaped projections. Based on a preliminary molecular phylogenetic analysis the reduction of keratinized oral structures in M. majori may have occurred convergently to that in M. mocquardi. The ecological data indicate that the tadpoles of the three most abundant species in Ranomafana (M. femoralis, M. majori and M. sp. 47) do not obviously differ in their choice of microhabitat although the differences in their oral structures indicate that they might use different food resources. They all show a preference for the stream areas with slow current and leaf litter substrate.
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Oro, Violeta, Magdalena Knezevic, Zoran Dinic, and Dusica Delic. "Bacterial Microbiota Isolated from Cysts of Globodera rostochiensis (Nematoda: Heteroderidae)." Plants 9, no. 9 (September 4, 2020): 1146. http://dx.doi.org/10.3390/plants9091146.
Повний текст джерелаАнотація:
The potato cyst nematode (PCN) Globodera rostochiensis is a plant parasite of potato classified into a group of quarantine organisms causing high economic losses worldwide. Due to the long persistence of the parasite in soil, cysts harbor numerous bacteria whose presence can lead to cyst death and population decline. The cysts of G. rostochiensis found in two potato fields were used as a source of bacteria. The universal procedure was applied to extract DNA from bacteria which was then sequenced with 16S primers. The aims of the study were to identify bacterial microbiota associated with the PCN populations and to infer their phylogenetic relationships based on the maximum likelihood and Bayesian phylogeny of the 16S sequences. In addition, the impact of the most significant climate and edaphic factors on bacterial diversity were evaluated. Regarding the higher taxonomy, our results indicate that the prevalent bacterial classes were Bacilli, Actinobacteria and Alphaproteobacteria. Phylogenetic analyses clustered Brevibacterium frigoritolerans within the family Bacillaceae, confirming its recent reclassification. Long-term climate factors, such as air temperature, insolation hours, humidity and precipitation, as well as the content of soil organic matter, affected the bacterial diversity. The ability of cyst nematodes to persist in soil for a long time qualifies them as a significant natural source to explore the soil bacterial microbiota.