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Akand, Md Kamrul Hasan, Mostafa Ali Reza Hossain, and Md Shariful Islam. "Present biodiversity status of loaches in the selected Hill-streams of Bangladesh." Research in Agriculture Livestock and Fisheries 2, no. 2 (September 16, 2015): 329–34. http://dx.doi.org/10.3329/ralf.v2i2.25018.
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A year-long survey was conducted to study the biodiversity status of freshwater loaches of Bangladesh. Data and sample collection were carried out in the hill-streams of Bangladesh in the three districts namely Sylhet, Netrokona and Dinajpur. Fish samples were also collected from Mymensingh district. The study was based on fish landing centre and fish market visit, on the spot data collection, interview of the fishermen and the fish traders, sample collection and secondary data collection. During the study, 12 loaches under 2 families were found. Among the collected loaches 8 are exclusively used as food fish and the rest 4 species can be considered as both food fish and ornamental fish. Among the total number of species found during the study, 2 loaches were threatened based on IUCN Red List. Among the loaches recorded in the survey, 2 are endangered (EN), 3 data deficient (DD) and 7 not threatened (NO). Among the collected loaches Botia dario, Botia lohachata and Lepidocephalichthys annandalei were very rare. The non-availability and less availability of some of the species indicate the alarming decline of the biodiversity of loaches in the surveyed area and in the country as a whole.Res. Agric., Livest. Fish.2(2): 329-334, August 2015
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Bamaniya, Dhaval C., A. Pavan-Kumar, P. Gireesh-Babu, Niti Sharma, Dhalongsaih Reang, Gopal Krishna, and W. S. Lakra. "DNA barcoding of marine ornamental fishes from India." Mitochondrial DNA Part A 27, no. 5 (February 23, 2015): 3093–97. http://dx.doi.org/10.3109/19401736.2014.1003923.
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Nuryanto, Agus, Kusbiyanto Kusbiyanto, and Dian Bhagawati. "Molecular barcoding of marine ornamental fish from the southern coast of West Java validates conventional identification." E3S Web of Conferences 322 (2021): 01004. http://dx.doi.org/10.1051/e3sconf/202132201004.
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Conventional identification of marine ornamental fish has faced difficulties due to similar color patterns of closed related species, or juvenile individuals have different color patterns from adult individuals. Molecular barcoding using the cytochrome c oxidase I (COI) gene provides a reliable tool for unmasking such difficulties. This study aimed to barcode marine ornamental fish from the southern coast of West Java. Fragment of the COI gene was sequenced from 54 morphotypes. In this study, we determined the taxonomic status of the samples based on a 5% genetic divergence, with the parameter including sequence percent identity, genetic distance, and length of monophyletic branch in a phylogenetic tree. The result showed that most samples had a high percentage of sequence identities, low genetic distances, and short chapters in monophyletic clades, but the remaining were not. Those data indicated that most samples could be identified at species-level without doubt and support conventional identification. Barcoding success is also depending on the availability of conspecific sequences in the databases. This study concluded that molecular barcoding could strengthen and validate traditional identification.
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Fahmi, Melta Rini, Ruby Vidia Kusumah, Idil Ardi, Shofihar Sinansari, and Eni Kusrini. "DNA BARCODING IKAN HIAS INTRODUKSI." Jurnal Riset Akuakultur 12, no. 1 (May 30, 2017): 29. http://dx.doi.org/10.15578/jra.12.1.2017.29-40.
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Identifikasi spesies menjadi tantangan dalam pengelolaan ikan hias introduksi baik untuk tujuan budidaya maupun konservasi. Penelitian ini bertujuan untuk melakukan identifikasi molekuler ikan hias introduksi yang beredar di pembudidaya dan pasar ikan hias Indonesia dengan menggunakan barcode DNA gen COI. Sampel ikan diperoleh dari pembudidaya dan importir ikan hias di kawasan Bandung dan Jakarta. Total DNA diekstraksi dari jaringan sirip ekor dengan menggunakan metode kolom. Amplifikasi gen target dilakukan dengan menggunakan primer FishF1, FishF2, FishR1, dan FishR2. Hasil pembacaan untai DNA disejajarkan dengan sekuen yang terdapat pada genbank melalui program BLAST. Identifikasi dilakukan melalui kekerabatan pohon filogenetik dan presentasi indeks kesamaan dengan sekuen genbank. Hasil identifikasi menunjukkan sampel yang diuji terbagi menjadi lima grup, yaitu: Synodontis terdiri atas lima spesies, Corydoras: empat spesies, Phseudoplatystoma: tiga spesies, Botia: tiga spesies, dan Leporinus: tiga spesies dengan nilai boostrap 99-100. Indeks kesamaan sekuen menunjukkan sebanyak 11 spesies memiliki indeks kesamaan 99%-100% dengan data genbank yaitu Synodontis decorus, Synodontis eupterus, Synodontis greshoffi, Botia kubotai, Botia lohachata, Rasbora erythromicron, Corydoras aeneus, Gyrinocheilus aymonieri, Eigenmannia virescens, Leporinus affinis, Phractocephalus hemioliopterus. Dua spesies teridentifikasi sebagai hasil hibridisasi (kawin silang) yaitu Leopard catfish (100% identik dengan Pseudoplatystoma faciatum) dan Synodontis leopard (100% identik dengan Synodontis notatus). Hasil analisis nukleotida penciri diperoleh tujuh nukleotida untuk Synodontis decora, 10 nukleotida untuk Synodontis tanganyicae, 13 nukleotida untuk Synodontis euterus, empat nukleotida untuk Synodontis notatus, dan 14 untuk Synodontis grashoffi. Kejelasan identifikasi spesies ikan menjadi kunci utama dalam budidaya, perdagangan, manajemen, konservasi, dan pengembangan ilmu pengetahuan.Species identification becomes a new challenge in the management of ornamental fish either for cultivation, or for conservation proposes. The objective of this study was to identify currently existing introduced ornamental fish in Indonesian farmers and markets using DNA barcodes COI gene. Fish samples were collected from farmers and importers of ornamental fish in Bandung and Jakarta. Total genome was extracted from caudal fin tissue using the column method. Amplification of the target gene was done by using FishF1, FishF2, FishR1, and FishR2 primers. DNA sequence was aligned with the sequences from genbank by BLAST program. Species identification was decided through the phylogenetic tree and similarity index with genbank sequences. The results showed that all of tested samples fall into five groups; Synodontis consisted of five species, Corydoras four species, Phseudoplatystoma four species, Botia three species, and Leporinus three species with 99-100 boostrap value. Sequence similarity index showed around 11 species have 99%-100% similarity index with sequence data on genbank which are Synodontis decorus, Synodontis eupterus, Synodontis greshoffi, Botia kubotai, Botia lohachata, Rasbora erythromicron, Corydoras aeneus, Gyrinocheilus aymonieri, Eigenmannia virescens, Leporinus affinis, Phractocephalus hemioliopterus. Two species were identified as hybridization product (interbreeding) including leopard catfish (100% identical with Pseudoplatystoma faciatum) and the leopard Synodontis (100% identical with Synodontis notatus). Analysis of nucleotide diagnostic showed Synodontis decora has seven nucleotides diagnostic, Synodontis tanganyicae 10 nucleotides, Synodontis euterus 13 nucleotides, Synodontis notatus four nucleotides, and Synodontis grashoffi 14 nucleotides. The correct identification of fish species is a useful tool for aquaculture, global marketing, management or conservation, and academic/scientific purpose.
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Steinke, Dirk, Tyler S. Zemlak, and Paul D. N. Hebert. "Barcoding Nemo: DNA-Based Identifications for the Ornamental Fish Trade." PLoS ONE 4, no. 7 (July 21, 2009): e6300. http://dx.doi.org/10.1371/journal.pone.0006300.
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Fahmi, Melta Rini, Anjang Bangun Prasetio, Ruby Vidia Kusumah, Erma Primanita Hayuningtyas, and Idil Ardi. "BARCODING DNA IKAN HIAS LAHAN GAMBUT." Jurnal Riset Akuakultur 11, no. 2 (December 28, 2016): 137. http://dx.doi.org/10.15578/jra.11.2.2016.137-145.
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Perairan gambut merupakan ekosistem unik yang memiliki kekayaan biodiversitas ikan, sebagian besar di antaranya memiliki potensi sebagai ikan hias. Penelitian ini dilakukan untuk melakukan identifikasi dan analisis keragaman genetik, karakter genetik, jarak genetik, dan pohon kekerabatan ikan-ikan yang mendiami perairan gambut Cagar Biosfere Bukit Batu Provinsi Riau. Tahap pertama penelitian ini adalah identifikasi secara morfologi terhadap 29 ikan hasil koleksi yang potensial sebagai ikan hias. Selanjutnya amplifikasi dan alignment 675 bp (base pair) dari 90 runutan parsial cytochrome c oxidase subunit 1 (COI). Hasil penelitian menunjukkan ikan yang diidentifikasi dapat dikelompokkan menjadi enam famili, yaitu Balontidae terdiri atas tiga spesies (12,5%); Cyprinidae 13 spesies (54,17%); Cobitidae satu spesies (4,17%); Siluridae dua spesies (8,3%); Datnoidae satu spesies (4,17%); dan Bagridae empat spesies (16,67%). Beberapa spesies memiliki perbedaan genetik intraspesies lebih dari 3%. Analisis kekerabatan dan clustering ikan hias lahan gambut berdasarkan gen COI memiliki nilai bootstrap 87-99 per ulangan.Peat is a unique ecosystem which a high fish biodiversity, and most of them are potential as ornamental fish. This research was conducted to identify and analyze genetic diversity, genetic code, genetic distances, and phylogenies of the fish that inhabit in the Bukit Batu Biosfere Reserves, Riau Province. The first stage of this study was identification of 29 fish species that potential as ornamental fish by using morphological character. The further stages were amplification and alignment of 675 base pairs of 90 partial sequences of cytochrome c oxidase subunit 1 (COI). Results showed that the identification based on COI could be classified into six families. These Families were Balontidae, Cyprinidae, Cobitidae, Siluridae, Datnoidae, and Bagridae which consist of three species (12.5%), 13 species (54.17%), one species (4.17%), two species (8.3%), one species (4.17%), and four species (16.67%), respectively. Some clustered have intra-species genetic divergence more than 3%. Phylogenetic and clustering analysis showed all of the OTU (0perational Taxonomic Unit) has a high bootstrap permutation of 87-99.
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Ložek, Filip, Jiří Patoka, and Martin Bláha. "Another hitchhiker exposed: Diceratocephala boschmai (Platyhelminthes: Temnocephalida) found associated with ornamental crayfish Cherax spp." Knowledge & Management of Aquatic Ecosystems, no. 422 (2021): 25. http://dx.doi.org/10.1051/kmae/2021023.
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There are known plenty tiny invertebrate species associated with decapod crustaceans. Our contribution documents the first record of New Guinean ornamental Cherax crayfish epibiont, Diceratocephala boschmai (Platyhelminthes: Temnocephalida) found in pet trade in the Czech Republic. Correct species assignment was confirmed by genetic barcoding. The pathway for introductions of organisms unintentionally moved in association with ornamental crayfish via the international trade has been highlighted. Although Cherax species survive in thermal waters in Europe, even potential introduction to these habitats posed threat to native crayfish ectosymbionts (branchiobdellids) thought similar ecological niche.
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Meilisza, Nina, Rina Hirnawati, Sulasy Rohmy, Agus Priyadi, and Jacques Slembrouck. "THE UTILIZATION OF THE KINDS OF LIVE FOOD ON CLOWN LOACH FISH JUVENILES (Chromobotia macracanthus Bleeker)." Indonesian Aquaculture Journal 6, no. 1 (June 30, 2011): 47. http://dx.doi.org/10.15578/iaj.6.1.2011.47-58.
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Domestication and mass production technology of clown loaches fish have been developed by the Research Institute for Ornamental Fish Culture, Depok and the Institute de Recherche pour le Developpement (IRD). In the process, some constraints has been found and one of them was the cost of production and sustainable supply of Artemia as the only one of live food which used for clown loaches post-larvae until 2-3 months old juvenile. To solve this constraints, the use of other live feed as a substitute or replacement of Artemia should be applied, caused by it research of the utilization of the kinds of live food on clown loach juvenile need to be done. This research aims to determine the kinds of live food which be recommended for the substitution of Artemia on clown loaches fish juvenile (Chromobotia macracanthus Bleeker). Research carried out using 1 month old clown loach juveniles designed into the Complete Randomized Design in two factors namely are class of fish size S (35-50 mg), M (55-70 mg), L (75-90 mg) and the kinds of live food in the form of Artemia as a control, Moina, mini maggot, blood worms (Chironomus), and silk worms (Tubifex). Three levels treatment by class of fish size factor and five levels treatment by the kinds of live food factor produce 15 kinds of interactions with duplications. The research was conducted at recirculation system for 8 weeks to 3 months old juveniles. Observations were carried and measuring the growth parameters including weight, total length of fish, as well as survival rate parameters based on the number of fish that live at the end of the research. The support is done by measuring the water quality of pH, DO, temperature, ammonia, conductivity, and nitrites, proximate analysis of feed also performed. The two of research step analyzed by ANOVA (Analysis of Variance) and continued by Tukey test.
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van der Walt, KA, T. Mäkinen, ER Swartz, and OLF Weyl. "DNA barcoding of South Africa’s ornamental freshwater fish – are the names reliable?" African Journal of Aquatic Science 42, no. 2 (August 21, 2017): 155–60. http://dx.doi.org/10.2989/16085914.2017.1343178.
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Kundu, Shantanu, Shibananda Rath, Kosygin Laishram, Avas Pakrashi, Ujjal Das, Kaomud Tyagi, Vikas Kumar, and Kailash Chandra. "DNA barcoding identified selected ornamental fishes in Murti river of East India." Mitochondrial DNA Part B 4, no. 1 (January 2, 2019): 594–98. http://dx.doi.org/10.1080/23802359.2018.1561220.
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Simoglou, Konstantinos B., Dimitrios N. Avtzis, Joaquín Baixeras, Ioanna Sarigkoli, and Emmanouil Roditakis. "Hylotelephium spectabile, a New Host for Carnation Tortrix Moth (Cacoecimorpha pronubana) and Molecular Characterization in Greece." Insects 12, no. 3 (March 15, 2021): 245. http://dx.doi.org/10.3390/insects12030245.
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Cacoecimorpha pronubana (Hübner) (Lepidoptera, Tortricidae) is a highly polyphagous pest of a wide range of crop and ornamental plants. It is of Mediterranean origin and widespread in European and Mediterranean Plant Protection Organization (EPPO) region. For the first time, infestations of Hylotelephium spectabile (Boreau) Ohba (syn.: Sedum spectabile Boreau) (Saxifragales, Crassulaceae) ornamental plants by C. pronubana larvae, in private gardens in urban area of Drama, Greece, were found. Species identification was conducted based on morphology of female genitalia. In addition, due to reports on occurrence of cryptic C. pronubana species within Europe, DNA barcoding was carried out to determine the molecular status of the pest. This communication reports a new host of C. pronubana and places the Greek pest population along with European species clade.
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Karpun, N. N., E. N. Zhuravleva, E. I. Shoshina, and N. I. Kirichenko. "The detection of an alien pest, the cotton leaf roller Haritalodes decorata (Lepidoptera: Crambidae), on the Black Sea Coast of Russia." Far Eastern entomologist 465 (November 2, 2022): 12–21. http://dx.doi.org/10.25221/fee.465.3.
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Here we report about the first finding of an alien pest, the cotton leaf roller Haritalodes derogata (Fabricius, 1775) (Lepidoptera: Crambidae), on the Russian Black Sea Coast. In summer of 2021, the significant damage caused by H. degorata to Hibiscus spp. was documented in the ornamental plantations of Sochi. The current distribution data and the bionomics of the species in the invaded region are provided. The DNA barcoding data obtained for the specimens from Sochi are analyzed comparing to the species representatives from the other parts of the world.
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HO, VT, TH NGUYEN, LBN NGUYEN, TTN NGUYEN, and MP NGUYEN. "COMPARISON OF rbcL AND trnH-psbA DNA BARCODES IN DIVERSE CAMELLIA SPECIES COLLECTION IN VIETNAM." SABRAO Journal of Breeding and Genetics 55, no. 3 (June 30, 2023): 877–85. http://dx.doi.org/10.54910/sabrao2023.55.3.22.
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Camellia is a large genus in the tea family of Theaceae. In this genus, several species serve different purposes, such as, medicinal and ornamental plants and beverage production. Thus, country-wide cultivation of various species of Camellia genus sought to alleviate poverty and promote economic development in many regions. However, studies on evaluating its genetic resources as a foundation for the conservation and development of this plant are yet to start. Currently, using DNA barcoding often serves as a highly reliable approach to identifying and characterizing numerous plants. In the presented study, a total of 10 Camellia accessions collected from Dong Bua village, Tam Quan commune, District Tam Dao, and Vinh Phuc province, Vietnam, underwent study during 2020–2022 at Ho Chi Minh City University of Food Industry, Vietnam. Evaluation of two DNA barcoding regions, namely, rbcL and trnH-psbA, transpired for their ability to distinguish the Camellia accessions belonging to different species in Vietnam. The results revealed a significant difference in the DNA sequences of the rbcL and trnH-psbA regions among the Camellia species. In addition, the trnH-psbA barcode region also showed higher effectiveness versus the rbcL region in recognizing various species of Camellia. The results authenticated the potential of DNA barcoding in the management, conservation, and development of the genetic resources of Camellia in Vietnam.
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Kolar, Antonija, Dora Hlebec, Katija Dolina, Milivoj Franjević, and Mladen Kučinić. "First DNA barcoding of a new alien species Glycaspis brimblecombei Moore, 1964 (Hemiptera: Aphalaridae) in Croatia with a distribution note." Ecologica Montenegrina 43 (July 1, 2021): 59–68. http://dx.doi.org/10.37828/em.2021.43.9.
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A new alien psyllid Glycaspis brimblecombei, native in Australia, was first discovered in Croatia in 2020. Its presence was also confirmed in the Botanical Garden of the Institute for Marine and Coastal Research (University of Dubrovnik) on the island of Lokrum, using DNA barcoding. Distribution and spreading of this alien species were noted as across the other continents so in Europe. The pest is considered as a threat to forestry, paper industry and could affect ornamental values of the eucalyptus species. It is important to continue with following research on this species because of the potential spreading and ascendant estimation.
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Chen, Zhenming, Ling Gao, Huizhong Wang, and Shangguo Feng. "Molecular Identification and Phylogenetic Analysis of Cymbidium Species (Orchidaceae) Based on the Potential DNA Barcodes matK, rbcL, psbA-trnH, and Internal Transcribed Spacer." Agronomy 14, no. 5 (April 29, 2024): 933. http://dx.doi.org/10.3390/agronomy14050933.
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Numerous Cymbidium species have significant commercial value globally due to their exotic ornamental flowers. Identifying Cymbidium species is challenging due to their similar shapes, which hinders their rational use and the conservation of germplasm resources. In the present study, firstly, four plastid loci (matK, rbcL, psbA-trnH, and atpF-atpH) and a nuclear locus (internal transcribed spacer, ITS) were initially examined to identify Cymbidium species. Secondly, we inferred the interspecific phylogeny of Cymbidium species using ITS sequences. All of these DNA regions, with the exception of atpF-atpH, could be readily amplified from Cymbidium, and the corresponding DNA sequences can be successfully obtained by sequencing. Our research demonstrated that ITS exhibited the highest intra- and interspecific divergences, the greatest barcoding gap, and the highest proportion of species identification. The phylogenetic analysis of Cymbidium species based on the ITS regions primarily corroborated the results obtained using traditional morphological methods. A comparative analysis of candidate DNA barcodes has shown that the ITS can be used not only for barcoding Cymbidium species but also for the phylogenetic analysis of Cymbidium.
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Jin, Dong-Pil, Sunhee Sim, Jong-Won Park, Ji-Eun Choi, Jiwon Yoon, Chae Eun Lim, and Min-Ha Kim. "Identification of the Plant Family Caryophyllaceae in Korea Using DNA Barcoding." Plants 12, no. 10 (May 22, 2023): 2060. http://dx.doi.org/10.3390/plants12102060.
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Caryophyllaceae is a large angiosperm family, with many species being utilized as ornamental or medicinal plants in Korea, in addition to several endangered species that are managed by the government. In this study, we used DNA barcoding for the accurate identification of Korean Caryophyllaceae. A total of 78 taxa (n = 215) were sequenced based on three chloroplast regions (rbcL, matK, and psbA–trnH) and nuclear ribosomal internal transcribed spacers (ITS). In the neighbor-joining tree, a higher accuracy of identification was generally observed when using ITS (>73%) rather than chloroplast regions (<62%). The highest resolution was found for rbcL + ITS (77.6%), although resolution varied according to the genus. Among the genera that included two and more species, five genera (Eremogone, Minuartia, Pseudostellaria, Sagina, and Stellaria) were successfully identified. However, the species of five other genera (Cerastium, Gypsophila, Dianthus, Silene, and Spergularia) showed relatively low resolutions (0–61.1%). In the cases of Cerastium, Dianthus, and Silene, ambiguous taxonomic relationships among unidentified species may have been a factor contributing to such low resolutions. However, in contrast to these results, Gypsophila and Spergularia have been identified well in previous studies. Our findings indicate the need of taxonomic reconsideration in Korea.
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Thi Hai, Yen Nguyen, Quang Ngo Xuan, Trong Nguyen Dinh, Phat Do Tien, and Mau Chu Hoang. "Morphology and DNA marker for distinguishing Paphiopedilum hangianum and Paphiopedilum emersonii from Vietnam." Journal of Experimental Biology and Agricultural Sciences 11, no. 2 (April 30, 2023): 423–35. http://dx.doi.org/10.18006/2023.11(2).423.435.
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Genus Paphiopedilum has species having lovely flowers which are incredibly attractive to everyone. Their ornamental and commercial value caused over-collection and illegal poaching and trade. Due to these reasons, nowadays, the Venus slipper orchids are facing to deplete in nature. Therefore, it is important to consider these species conservation. Mainly, it is necessary to prioritize the identification and phylogenetic analysis methods of the genus Paphiopedilum which includes many species with similar morphological characteristics. Consequently, it isn't easy to distinguish the identical species of this genus when the plants are young or not yet fully flowering. Therefore, this study aimed to distinguish two Paphiopedilum species, i.e. P. hangianum and P. emersonii, which have similar morphological characteristics, through comparative morphological analysis and differences in DNA barcoding sequences. To solve the problem associated with species identifications, a morphological comparison table was created with the four DNA sequence markers matK, rbcL, rpoC1 and trnH-psbA. The results of the morphological analysis showed that P. hangianum and P. emersonii are significantly different from each other in the flower's characteristics. While the difference in leaf morphology of both selected species is found very little, it is also distinguishable upon careful comparison. Moreover, the DNA barcoding indicator gave accurate and rapid distinctions between the two species, even when the plants are young or without flowers. Furthermore, this DNA barcoding can establish an evolutionary relationship between the two selected species and the other species of the genus Paphiopedilum. The results of this study also suggested that the indicator trnH-psbA is a suitable marker for distinguishing these two species and can be applied for the phylogenetic analysis of the genus Paphiopedilum in Vietnam.
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O. Elansary, Hosam, Muhammad Ashfaq, Hayssam M. Ali, and Kowiyou Yessoufou. "The first initiative of DNA barcoding of ornamental plants from Egypt and potential applications in horticulture industry." PLOS ONE 12, no. 2 (February 15, 2017): e0172170. http://dx.doi.org/10.1371/journal.pone.0172170.
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Consoli, Erika, Andrea C. Ruthes, Eder Reinhard, and Paul Dahlin. "First Morphological and Molecular Report of Aphelenchoides blastophthorus on Strawberry Plants in Switzerland." Plant Disease 103, no. 11 (November 2019): 2851–56. http://dx.doi.org/10.1094/pdis-07-18-1241-re.
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Foliar nematodes represent a minor feeding group within the genus Aphelenchoides Fischer, 1894. The facultative plant parasitic species A. blastophthorus can cause crinkling of leaves, reduced vigor, and stunting of agricultural and ornamental plants. Here we report the first finding of A. blastophthorus in leaves, crowns, and roots of strawberry plants collected in Switzerland in 2018. Species identification was confirmed by morphological and morphometric characterization supported by molecular barcoding of 18S ribosomal RNA (18S), 28S ribosomal RNA (28S), and cytochrome c oxidase I (COI) gene fragment analyses. Phylogenetic analysis of 18S indicated that A. blastophthorus was grouped within close distance to A. fragariae, a well-known foliar nematode affecting strawberry plants. Furthermore, the newly generated molecular barcodes of the partial 28S and COI of A. blastophthorus will support species identification in the future.
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Sari, Dini Wahyu Kartika, Himawan Achmad, Hafit Rahman, and Harya Bimasuci. "Molecular Identification of Several Morphologically Distinct Flowerhorn Fish (Family) Using Mitochondrial <i>COI</i> Gene Marker." Journal of Tropical Biodiversity and Biotechnology 8, no. 2 (May 22, 2023): 78459. http://dx.doi.org/10.22146/jtbb.78459.
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Flowerhorn fish has been known as a breed of fish produced by artificial hybridization between several cichlid fish. Other ornamental cichlid fish generally known to be crossed to make flowerhorn variant includes Amphilophus citrinelus, Amphilophus labiatus, Vieja melanurus, and Amphilophus trimaculatus. Our study identified a variety of flowerhorn samples with distinct morphotypes, dubbed as Cencu (LH1CC), Kamfa (LH2KF), Thai Silk (LH3TS), Kirin (LH4KR), Parrot (LH5PR), and Vieja (LH6VJ) using mtDNA COI-based DNA barcoding. Molecular analysis and phylogenetics showed that all sample had 0% genetic divergence and conspecific with A. trimaculatus sequence. Hence, we concluded that despite having varied morphotypes, all flowerhorn samples were identified as A. trimaculatus and were a variation of flowerhorn from A. trimaculatus lineage. The findings should be used as a precaution as the fish is identified as an invasive species.
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Chen, Jinliao, Fei Wang, Chengyuan Zhou, Sagheer Ahmad, Yuzhen Zhou, Minghe Li, Zhongjian Liu, and Donghui Peng. "Comparative Phylogenetic Analysis for Aerides (Aeridinae, Orchidaceae) Based on Six Complete Plastid Genomes." International Journal of Molecular Sciences 24, no. 15 (August 5, 2023): 12473. http://dx.doi.org/10.3390/ijms241512473.
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Aerides Lour. (Orchidaceae, Aeridinae) is a group of epiphytic orchids with high ornamental value, mainly distributed in tropical and subtropical forests, that comprises approximately 20 species. The species are of great value in floriculture and garden designing because of their beautiful flower shapes and colors. Although the morphological boundaries of Aerides are clearly defined, the relationship between Aerides and other closely related genera is still ambiguous in terms of phylogeny. To better understand their phylogenetic relationships, this study used next-generation sequencing technology to investigate the phylogeny and DNA barcoding of this taxonomic unit using genetic information from six Aerides plastid genomes. The quadripartite-structure plastomes ranged from 147,244 bp to 148,391 bp and included 120 genes. Among them, 74 were protein coding genes, 38 were tRNA genes and 8 were rRNA genes, while the ndh genes were pseudogenized or lost. Four non-coding mutational hotspots (rpl20–rpl33, psbM, petB, rpoB–trnCGCA, Pi > 0.06) were identified. A total of 71–77 SSRs and 19–46 long repeats (>30 bp) were recognized in Aerides plastomes, which were mostly located in the large single-copy region. Phylogenetic analysis indicated that Aerides was monophylic and sister to Renanthera. Moreover, our results confirmed that six Aerides species can be divided into three major clades. These findings provide assistance for species identification and DNA barcoding investigation in Aerides, as well as contributes to future research on the phylogenomics of Orchidaceae.
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GARCÍA DÁVILA, Carmen Rosa, Mayra Almendra FLORES SILVA, Lucero PINEDO TENAZOA, Rodrigo LOYOLA LLORI, and Diana CASTRO RUIZ. "APLICACIÓN DEL BARCODING AL MANEJO Y CONSERVACIÓN DE PECES Y SUS SUBPRODUCTOS EN LA AMAZONÍA PERUANA." Folia Amazónica 26, no. 2 (November 30, 2018): 195–204. http://dx.doi.org/10.24841/fa.v26i2.329.
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Fue generado y depositado en el GenBank secuencias nucleotidicas del gen COI de 207 especies de peces comercializados en los mercados de consumo y ornamental en la Amazonia peruana. Posteriormente este banco de secuencias nucleotídicas fueron utilizadas como base de comparación en la identificación específica exitosa de: i) larvas de bagres colectadas en tres cuencas hidrológicas (Ucayali, Napo y Marañón), mostrando ser una alternativa mucho más segura que las determinaciones mediante análisis morfológico o morfométrico; ii) de alevinos de identidad morfológica dudosa en los procesos de exportación, mostrando que la identidad específica de juveniles de saltón blanco B. filamentosun y saltón negro B. capapretum asignada a priori por los extractores era equivocada y iii) subproductos de peces amazónicos, lo que permitió mostrar los altos grados de sustitución en filete fresco. La generación de estos banco de secuencias nos permitió proponer protocolos basados en caracterización molecular de las especies, lo que pensamos contribuirá a la modernización del sistema de fiscalización y monitoreo de la comercialización de los peces (ornamentales y de consumo), permitiéndole los decisoras de política un mayor control tanto en el área de comercialización como de manejo sostenido y conservación en el sector pesquero en la Amazonía peruana.
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Abd-Rabou, S., H. Shalaby, J. F. Germain, N. Ris, P. Kreiter, and T. Malausa. "Identification of mealybug pest species (Hemiptera: Pseudococcidae) in Egypt and France, using a DNA barcoding approach." Bulletin of Entomological Research 102, no. 5 (February 24, 2012): 515–23. http://dx.doi.org/10.1017/s0007485312000041.
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AbstractPseudococcidae (mealybugs) is a large taxonomic group, including a number of agronomic pests. Taxonomic identification of mealybug species is a recurrent problem and represents a major barrier to the establishment of adequate pest management strategies. We combined molecular analysis of three DNA markers (28S-D2, cytochrome oxidase I and internal transcribed spacer 2) with morphological examination, for the identification of 176 specimens collected from 40 mealybug populations infesting various crops and ornamental plants in Egypt and France. This combination of DNA and morphological analyses led to the identification of 17 species: seven in Egypt (Planococcus citri (Risso), Planococcus ficus (Signoret), Maconellicoccus hirsutus (Green), Ferrisia virgata (Cockerell), Phenacoccus solenopsis Tinsley, Phenacoccus parvus Morrison and Saccharicoccus sacchari (Cockerell)) and 11 in France (Planococcus citri, Pseudococcus viburni Signoret, Pseudococcus longispinus (Targioni-Tozzetti), Pseudococcus comstocki (Kuwana), Rhizoecus amorphophalli Betrem, Trionymus bambusae (Green), Balanococcus diminutus (Leonardi), Phenacoccus madeirensis Green, Planococcus vovae (Nasonov), Dysmicoccus brevipes (Cockerell) and Phenacoccus aceris Signoret), Pl. citri being found in both countries. We also found genetic variation between populations considered to belong to the same species, justifying further investigation of the possible occurrence of complexes of cryptic taxa.
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Fahmi, Melta R., Eni Kusrini, Erma P. Hayuningtiyas, Shofihar Sinansari, and Rudhy Gustiano. "DNA BARCODING USING COI GENE SEQUENCES OF WILD BETTA FIGHTING FISH FROM INDONESIA: PHYLOGENY, STATUS AND DIVERSITY." Indonesian Fisheries Research Journal 26, no. 2 (December 7, 2020): 97. http://dx.doi.org/10.15578/ifrj.26.2.2020.97-105.
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The wild betta fish is a potential ornamental fish export commodity normally caught by traders or hobbyists in the wild. However, the population of wild betta in nature has declined and become a threat for their sustainability. This research was conducted to analyze the genetic diversity, phylogenetic relationships, and molecular identification through DNA COI gene sequence of Indonesian wild betta fish. A total of 92 wild betta fish specimens were collected in this study. Amplification of COI genes was carried out using Fish F1, Fish R1, Fish F2, and Fish R2 primers. The genetic diversity and phylogenetic relationships were analyzed using MEGA version 5 software program. Species identification of the specimen was conducted using BLAST program with 98-100% similarity value of the DNA sequences to indicate the same species. Phylogenetic tree construction showed seven monophyletic clades and showed that Betta smaragdina was the ancestral species of genus Betta in Indonesian waters. Genetic distance among species ranged from 0.02 to 0.30, whereas intra-species genetic distance ranged from 0 to 6.54.
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Li, Wenlan, Qiqi Ren, Jian Feng, Shiou Yih Lee, and Yangyang Liu. "DNA barcoding for the identification and authentication of medicinal deer (Cervus sp.) products in China." PLOS ONE 19, no. 1 (January 19, 2024): e0297164. http://dx.doi.org/10.1371/journal.pone.0297164.
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Deer products from sika deer (Cervus nippon) and red deer (C. elaphus) are considered genuine and used for Traditional Chinese Medicine (TCM) materials in China. Deer has a very high economic and ornamental value, resulting in the formation of a characteristic deer industry in the prescription preparation of traditional Chinese medicine, health food, cosmetics, and other areas of development and utilization. Due to the high demand for deer products, the products are expensive and have limited production, but the legal use of deer is limited to only two species of sika deer and red deer; other wild deer are prohibited from hunting, so there are numerous cases of mixing and adulteration of counterfeit products and so on. There have been many reports that other animal (pig, cow, sheep, etc.) tissues or organs are often used for adulteration and confusion, resulting in poor efficacy of deer traditional medicine and trade fraud in deer products. To authenticate the deer products in a rapid and effective manner, the analysis used 22 deer products (antler, meat, bone, fetus, penis, tail, skin, and wool) that were in the form of blind samples. Total DNA extraction using a modified protocol successfully yielded DNA from the blind samples that was useful for PCR. Three candidate DNA barcoding loci, cox1, Cyt b, and rrn12, were evaluated for their discrimination strength through BLAST and phylogenetic clustering analyses. For the BLAST analysis, the 22 blind samples obtained 100% match identity across the three gene loci tested. It was revealed that 12 blind samples were correctly labeled for their species of origin, while three blind samples that were thought to originate from red deer were identified as C. nippon, and seven blind samples that were thought to originate from sika deer were identified as C. elaphus, Dama dama, and Rangifer tarandus. DNA barcoding analysis showed that all three gene loci were able to distinguish the two Cervus species and to identify the presence of adulterant species. The DNA barcoding technique was able to provide a useful and sensitive approach in identifying the species of origin in deer products.
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Alam, Md Shahin, Nadim Haidar, Maliha Khanom, and Mst Kaniz Fatema. "Fish Biodiversity and Suggested Conservation Measures of Transboundary River Someshwari in Netrokona, Bangladesh." Asian Journal of Fisheries and Aquatic Research 26, no. 5 (May 17, 2024): 61–70. http://dx.doi.org/10.9734/ajfar/2024/v26i5766.
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Considering the importance of fish biodiversity for sustainable management of river fisheries, this study aims to explore and evaluate the fish biodiversity of Someshwari River along with conservation measures from November 2020 to October 2021. Data collection was carried out in Jaria, Susang Durgapur, Shivganj Bazar and Bijoypur of Netrokona district. Questionnaire interview, Focus Group Discussion (FGD), Direct observations, Key Informant Interview (KII) was used to collect data. During the study period, 23 species under 12 families were determined. Among them 6 finfish species are endangered, 4 are critically endangered, 5 are vulnerable, 7 are data deficient, and 2 are not threatened, respectively which includes highest catch catfishes at about 26.62%. However, the lowest amount catch constituted the Miror carp of about 5.29%. After the catfish, the second highest catch was 15.9% of small prawn. Another dominant group major carps contained 11.26%, and barbs remained at 11% of the catch and the loaches constituted 1.3% of the total catch. In addition, other groups like Mola carplet 7%, gourami 2.20%, Spiny eels 9.86% etc. were found in the Someshwari river. There were about 81% fish for food and 17% ornamental fish. Fourteen distinct types of fishing equipment were used namely: nets, traps, hooks, and lines, and wounding equipment. Finally, indiscriminate use of harmful gear, extraction of sand and rock, inadequate supervision of Governments and Non Governemental orgazizations, pollution from the adjacent areas, high interest rate of bank loan were understood as common constraints in the study area. Therefore, recommendations were made to improve river fisheries management through habitat restoration, increasing public awareness, prohibition on exploiting brood fish and active participation for sustainable catch.
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Razuvaeva, A. V., E. G. Ulyanova, E. S. Skolotneva, and I. V. Andreeva. "Species identification of spider mites (Tetranychidae: Tetranychinae): a review of methods." Vavilov Journal of Genetics and Breeding 27, no. 3 (June 2, 2023): 240–49. http://dx.doi.org/10.18699/vjgb-23-30.
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Spider mites (Acari: Tetranychidae) are dangerous pests of agricultural and ornamental crops, the most economically significant of them belonging to the genera Tetranychus, Eutetranychus, Oligonychus and Panonychus. The expansion of the distribution areas, the increased harmfulness and dangerous status of certain species in the family Tetranychidae and their invasion of new regions pose a serious threat to the phytosanitary status of agroand biocenoses. Various approaches to acarofauna species diagnosis determine a rather diverse range of currently existing methods generally described in this review. Identification of spider mites by morphological traits, which is currently considered the main method, is complicated due to the complexity of preparing biomaterials for diagnosis and a limited number of diagnostic signs. In this regard, biochemical and molecular genetic methods such as allozyme analysis, DNA barcoding, restriction fragment length polymorphism (PCR-RFLP), selection of species-specific primers and real-time PCR are becoming important. In the review, close attention is paid to the successful use of these methods for species discrimination in the mites of the subfamily Tetranychinae. For some species, e. g., the two-spotted spider mite (Tetranychus urticae), a range of identification methods has been developed – from allozyme analysis to loop isothermal amplification (LAMP), while for many other species a much smaller variety of approaches is available. The greatest accuracy in the identification of spider mites can be achieved using a combination of several methods, e. g., examination of morphological features and one of the molecular approaches (DNA barcoding, PCR-RFLP, etc.). This review may be useful to specialists who are in search of an effective system for spider mite species identification as well as when developing new test systems relevant to specific plant crops or a specific region.
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Bourret, Tyler B., Sebastian N. Fajardo, Cole P. Engert, and David M. Rizzo. "A Barcode-Based Phylogenetic Characterization of Phytophthora cactorum Identifies Two Cosmopolitan Lineages with Distinct Host Affinities and the First Report of Phytophthora pseudotsugae in California." Journal of Fungi 8, no. 3 (March 16, 2022): 303. http://dx.doi.org/10.3390/jof8030303.
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A collection of 30 Phytophthora cactorum and 12 P. pseudotsugae (subclade 1a) strains isolated from several recent surveys across California was phylogenetically compared to a worldwide collection of 112 conspecific strains using sequences from three barcoding loci. The surveys baited P. cactorum from soil and water across a wide variety of forested ecosystems with a geographic range of more than 1000 km. Two cosmopolitan lineages were identified within the widespread P. cactorum, one being mainly associated with strawberry production and the other more closely associated with apple orchards, oaks and ornamental trees. Two other well-sampled P. cactorum lineages, including one that dominated Californian restoration outplantings, were only found in the western United States, while a third was only found in Japan. Coastal California forest isolates of both Phytophthora species exhibited considerable diversity, suggesting both may be indigenous to the state. Many isolates with sequence accessions deposited as P. cactorum were determined to be P. hedraiandra and P. ×serendipita, with one hybrid lineage appearing relatively common across Europe and Asia. This study contains the first report of P. pseudotsugae from the state of California and one of the only reports of that species since its original description.
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A. Salim, Mohamed. "Morpho-Molecular Study on some Taxa of Apocynaceae Sensu Lato." International Journal of Agriculture and Biology 25, no. 05 (May 1, 2021): 1111–19. http://dx.doi.org/10.17957/ijab/15.1770.
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Apocynaceae sensu lato (s.l.) is treated as distinct family in some taxonomic systems while in others is treated as two separated families viz. Apocynaceae sensu stricto (s.s.) and Asclepiadaceae. So the main objective of the present study was to adopt one of the two views. The morphological characters viz. whole plant, lamina vein architecture and lamina epidermal characters of 20 wild and ornamental species were examined using LM and SEM. The data were numerically analyzed to detect the phenetic relationship among the studied species. DNA barcoding based on the sequencing of rbcL gene was cladistically analyzed to detect the phylogenetic relationship among the studied species. The generated phenogram showed a clear separation of two subseries; one of them belonged to Apocynaceae and the other with the remaining taxa belonging to Asclepiadaceae. The obtained cladogram showed that all of the studied species were divided into four lineages. It is concluded that the phenetic analysis supports the treatment of Apocynaceae s.l. as two distinct families; Apocynaceae s.s. Asclepiadaceae contrary of the phylogenetic one that supports the treatment of Apocynaceae s.s. and Asclepiadaceae as one family (Apocynaceae s.l.) with four subfamilies viz. Apocynoideae, Rauvolfiodeae, Asclepiadoideae and Periplocoideae. © 2021 Friends Science Publishers
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Nguyen, Nhu-Hoa, Huyen-Trang Vu, Ngoc-Diep Le, Thanh-Diem Nguyen, Hoa-Xo Duong, and Hoang-Dung Tran. "Molecular Identification and Evaluation of the Genetic Diversity of Dendrobium Species Collected in Southern Vietnam." Biology 9, no. 4 (April 10, 2020): 76. http://dx.doi.org/10.3390/biology9040076.
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Dendrobium has been widely used not only as ornamental plants but also as food and medicines. The identification and evaluation of the genetic diversity of Dendrobium species support the conservation of genetic resources of endemic Dendrobium species. Uniquely identifying Dendrobium species used as medicines helps avoid misuse of medicinal herbs. However, it is challenging to identify Dendrobium species morphologically during their immature stage. Based on the DNA barcoding method, it is now possible to efficiently identify species in a shorter time. In this study, the genetic diversity of 76 Dendrobium samples from Southern Vietnam was investigated based on the ITS (Internal transcribed spacer), ITS2, matK (Maturase_K), rbcL (ribulose-bisphosphate carboxylase large subunit) and trnH-psbA (the internal space of the gene coding histidine transfer RNA (trnH) and gene coding protein D1, a polypeptide of the photosystem I reaction center (psaB)) regions. The ITS region was found to have the best identification potential. Nineteen out of 24 Dendrobium species were identified based on phylogenetic tree and Indel information of this region. Among these, seven identified species were used as medicinal herbs. The results of this research contributed to the conservation, propagation, and hybridization of indigenous Dendrobium species in Southern Vietnam.
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Abi Saad, Charlie, Mario Masiello, Wassim Habib, Elvis Gerges, Simona Marianna Sanzani, Antonio Francesco Logrieco, Antonio Moretti, and Stefania Somma. "Diversity of Fusarium Species Isolated from Symptomatic Plants Belonging to a Wide Range of Agri-Food and Ornamental Crops in Lebanon." Journal of Fungi 8, no. 9 (August 23, 2022): 897. http://dx.doi.org/10.3390/jof8090897.
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Lebanon is a small Mediterranean country with different pedoclimatic conditions that allow the growth of both temperate and tropical plants. Currently, few studies are available on the occurrence and diversity of Fusarium species on Lebanese crops. A wide population of Fusarium strains was isolated from different symptomatic plants in the last 10 years. In the present investigation, a set of 134 representative strains were molecularly identified by sequencing the translation elongation factor, used in Fusarium as a barcoding gene. Great variability was observed, since the strains were grouped into nine different Fusarium Species Complexes (SCs). Fusarium oxysporum SC and Fusarium solani SC were the most frequent (53% and 24%, respectively). Members of important mycotoxigenic SCs were also detected: F. fujikuroi SC (7%), F. sambucinum SC (5%), F. incarnatum-equiseti SC (3%), and F. tricinctum SC (4%). Two strains belonging to F. lateritium SC, a single strain belonging to F. burgessii SC, and a single strain belonging to F. redolens SC were also detected. This paper reports, for the first time, the occurrence of several Fusarium species on Lebanese host plants. The clear picture of the Fusarium species distribution provided in this study can pose a basis for both a better understanding of the potential phytopathological and toxicological risks and planning future Fusarium management strategies in Lebanon.
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Vu, Huyen-Trang, Quoc-Luan Vu, Thanh-Diem Nguyen, Ngan Tran, Thanh-Cong Nguyen, Phuong-Nam Luu, Duy-Duong Tran, Truong-Khoa Nguyen, and Ly Le. "Genetic Diversity and Identification of Vietnamese Paphiopedilum Species Using DNA Sequences." Biology 9, no. 1 (December 31, 2019): 9. http://dx.doi.org/10.3390/biology9010009.
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Paphiopedilum is among the most popular ornamental orchid genera due to its unique slipper flowers and attractive leaf coloration. Most of the Paphiopedilum species are in critical danger due to over-exploitation. They were listed in Appendix I of the Convention on International Trade in Endangered Species of Wild Fauna and Flora, which prevents their being traded across borders. While most Paphiopedilum species are distinctive, owing to their respective flowers, their vegetative features are more similar and undistinguished. Hence, the conservation of these species is challenging, as most traded specimins are immature and non-flowered. An urgent need exists for effective identification methods to prevent further illegal trading of Paphiopedilum species. DNA barcoding is a rapid and sensitive method for species identification, at any developmental stage, using short DNA sequences. In this study, eight loci, i.e., ITS, LEAFY, ACO, matK, trnL, rpoB, rpoC1, and trnH-psbA, were screened for potential barcode sequences on the Vietnamese Paphiopedilum species. In total, 17 out of 22 Paphiopedilum species were well identified. The studied DNA sequences were deposited to GenBank, in which Paphiopedilum dalatense accessions were introduced for the first time. ACO, LEAFY, and trnH-psbA were limited in amplification rate for Paphiopedilum. ITS was the best single barcode. Single ITS could be used along with nucleotide polymorphism characteristics for species discrimination. The combination of ITS + matK was the most efficient identification barcode for Vietnamese Paphiopedilum species. This barcode also succeeded in recognizing misidentified or wrongly-named traded samples. Different bioinformatics programs and algorithms for establishing phylogenetic trees were also compared in the study to propose quick, simple, and effective tools for practical use. It was proved that both the Bayesian Inference method in the MRBAYES program and the neighbor-joining method in the MEGA software met the criteria. Our study provides a barcoding database of Vietnamese Paphiopedilum which may significantly contribute to the control and conservation of these valuable species.
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Rha'ifa, Febrina Amaliya, Deiandra Jasmine Audrea, Lukman Hakim, and Tuty Arisuryanti. "DNA Barcode of Barred Mudskipper (Periophthalmus argentilineatus Valenciennes, 1837) from Tekolok Estuary (West Nusa Tenggara, Indonesia) and Their Phylogenetic Relationship with Other Indonesian Barred Mudskippers." Journal of Tropical Biodiversity and Biotechnology 6, no. 2 (May 20, 2021): 59702. http://dx.doi.org/10.22146/jtbb.59702.
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Barred mudskipper (Periophthalmus argentilineatus) has a potency to be developed as protein for human consumption and ornamental fish. The fish also has an important role in mangrove ecosystems. Nevertheless, many barred mudskippers have been considered a cryptic species. Therefore, accurate identification is needed to clarify species identification of the barred mudskipper using DNA barcoding. This research aimed to identify barred mudskippers from Tekolok Estuary (East Lombok, West Nusa Tenggara, Indonesia) using COI mitochondrial gene as a DNA barcode and analyze genetic relationship with other barred mudskippers from several regions of Indonesia recorded in GenBank. This study used a PCR method with universal primers FishF2 and FishR2. The data was then analysed using DNASTAR, BLAST, Mesquite, MEGA, DnaSP, BEAST, GenAlEx, and NETWORK. The results revealed that barred mudskipper from Tekolok Estuary has been verified as Periophthalmus argentilineatus. The results also exhibited that P. argentilineatus from Tekolok Estuary has a close genetic relationship to P.argentilineatus from Tukad Bilukpoh (Jembrana, Bali). In addition, phylogenetic analysis showed that P.argentilineatus from Indonesia consisted of two clades with a genetic distance of approximately 6.64%. This analysis revealed evidence of the cryptic diversity of P.argentilineatus from Indonesia. Further detailed studies are needed to clarify whether Indonesian P.argentilineatus should be categorized into more than one species or single species with several subspecies.
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Ma, Qiuyue, Yanan Wang, Lu Zhu, Changwei Bi, Shuxian Li, Shushun Li, Jing Wen, Kunyuan Yan, and Qianzhong Li. "Characterization of the Complete Chloroplast Genome of Acer truncatum Bunge (Sapindales: Aceraceae): A New Woody Oil Tree Species Producing Nervonic Acid." BioMed Research International 2019 (November 24, 2019): 1–13. http://dx.doi.org/10.1155/2019/7417239.
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Acer truncatum, which is a new woody oil tree species, is an important ornamental and medicinal plant in China. To assess the genetic diversity and relationships of A. truncatum, we analyzed its complete chloroplast (cp) genome sequence. The A. truncatum cp genome comprises 156,492 bp, with the large single-copy, small single-copy, and inverted repeat (IR) regions consisting of 86,010, 18,050, and 26,216 bp, respectively. The A. truncatum cp genome contains 112 unique functional genes (i.e., 4 rRNA, 30 tRNA, and 78 protein-coding genes) as well as 78 simple sequence repeats, 9 forward repeats, 1 reverse repeat, 5 palindromic repeats, and 7 tandem repeats. We analyzed the expansion/contraction of the IR regions in the cp genomes of six Acer species. A comparison of these cp genomes indicated the noncoding regions were more diverse than the coding regions. A phylogenetic analysis revealed that A. truncatum is closely related to A. miaotaiense. Moreover, a novel ycf4-cemA indel marker was developed for distinguishing several Acer species (i.e., A. buergerianum, A. truncatum, A. henryi, A. negundo, A. ginnala, and A. tonkinense). The results of the current study provide valuable information for future evolutionary studies and the molecular barcoding of Acer species.
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Murniasih, Siti, Dedi Jusadi, Mia Setiawati, and Sri Nuryati. "Dietary free glutamine supplementation to increase physiological responses and survival rate of clown loach juvenile, Chromobotia macracanthus Bleeker, 1852." Jurnal Iktiologi Indonesia 19, no. 3 (October 1, 2019): 437. http://dx.doi.org/10.32491/jii.v19i3.466.
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Clown loach Chromobotia macracanthus is one of Indonesian native species and as a key species for ornamental aquaculture. The problem in mass production of this species are the low of growth rate which causes a long period of rearing and low of survival rate. The purpose of the present study was to evaluate free glutamine supplementation at different doses in diet to increase physiological response, growth performance and survival rate of clown loach. Expe-rimental diets contained four different free glutamine levels, viz 0, 1, 2 and 3%. These diets were given to six repli-cate groups of 50 juvenile clown loaches. The fish were reared in each aquarium with dimensions of 40×30×30 cm3 for 60 days. Fish were fed four times a day at satiation. Parameters observed including intestinal glutamine concen-tration, villous and intestinal morphometry, intestinal protease activity, feed efficiency, nutrient retention, growth performance, survival rate, superoxide dismutase (SOD) activity, and malondialdehyde (MDA). The results showed that supplementation of 1% free glutamine significantly affected the morphometry of villi. The length and surface area of villi at a dose of 1% showed the highest values i.e., 320.44 ± 10.39 μm and 27,046.79 ± 250.54 μm2, respect-ively. The 1% dose also had a significant effect on protease activity (13.57 ± 1.92 mg units of protein-1) compared to the 0% dose. The 2% dose showed the highest SOD activity (0.82 ± 0.07 mg protein-1 unit) and the lowest MDA level was found at a dose of 3% (0.25 ± 0.02 nmol mg protein-1). Feed consumption with the supplementation of free glutamine has a significant effect on survival rate with the highest value reached 97.00 ± 1.00%, but no significant effect on intestinal morphometry, feed efficiency, nutrient retention and growth performance. Dietary with the sup-plementation of free glutamine is not able to improve growth performance, but can improve the physiological res-ponse and survival rate.
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Kostas, Stefanos, Stefanos Hatzilazarou, Elias Pipinis, Soumaya Bourgou, Imtinen Ben Haj Jilani, Wafa Ben Othman, Wided Megdiche-Ksouri, et al. "DNA Barcoding, GIS-Facilitated Seed Germination and Pilot Cultivation of Teucrium luteum subsp. gabesianum (Lamiaceae), a Tunisian Local Endemic with Potential Medicinal and Ornamental Value." Biology 11, no. 3 (March 17, 2022): 462. http://dx.doi.org/10.3390/biology11030462.
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In the context of plant conservation and sustainable use of unique neglected and underutilized phytogenetic resources, this study focused on the Tunisian local endemic Teucrium luteum subsp. gabesianum (Lamiaceae). Using Geographical Information Systems and online databases, detailed taxon-specific ecological profiling was produced for the first time, which illustrated the temperature and climate conditions in its wild habitats and facilitated the investigation of how temperature affects its seed germination, thus making its cultivation in anthropogenic environments possible. Following the seed propagation first reported herein (77.5–81.25% at temperatures between 15 and 25 °C), species-specific in situ and ex situ conservation efforts or sustainable exploitation strategies can be enabled. This study also reported for the first time how chemical and integrated nutrient management (INM) fertilizers affect the growth and pilot cultivation of its seedlings (INM more advantageous). The firstly-reported herein DNA barcoding may enable its traceability, allowing future product design. The multidisciplinary approach followed has paved the way to bridge important research gaps hindering conservation efforts and/or the sustainable exploitation of this local Tunisian endemic plant to date. Based on the aforementioned results, the feasibility and readiness timescale for its sustainable exploitation was overviewed and re-evaluated herein, upgrading (>two-fold) its potential value for the medicinal-cosmetic, agro-alimentary, and ornamental-horticultural sectors.
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KIRICHENKO, NATALIA, PAOLO TRIBERTI, EVGENIY AKULOV, MARGARITA PONOMARENKO, SVETLANA GOROKHOVA, VIKTOR SHEIKO, ISSEI OHSHIMA, and CARLOS LOPEZ-VAAMONDE. "Exploring species diversity and host plant associations of leaf-mining micromoths (Lepidoptera: Gracillariidae) in the Russian Far East using DNA barcoding." Zootaxa 4652, no. 1 (August 7, 2019): 1–55. http://dx.doi.org/10.11646/zootaxa.4652.1.1.
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The Russian Far East (RFE) is an important hotspot of biodiversity whose insect fauna remains understudied, particularly its Microlepidoptera. Here we explore the diversity of leaf-mining micromoths of the family Gracillariidae, their distribution and host plant associations in RFE using a combination of field observations and sampling, DNA barcoding, morphological analysis and literature review. We collected 91 gracillariid specimens (45 larvae, 9 pupae and 37 adults) in 12 localities across RFE and identified 34 species using a combination of DNA barcoding and morphology. We provide a genetic library of 57 DNA barcodes belonging to 37 Barcode Index Numbers (BINs), including four BINs that could potentially represent species new to science. Leaf mines and leaf shelters are described and illustrated for 32 studied species, male or female genitalia as well as forewing patterns of adults are shown, especially for those species identified based on morphology. Three species, Micrurapteryx caraganella (Hering), Callisto insperatella (Nickerl), and Phyllonorycter junoniella (Zeller) are newly recorded from RFE. Five species previously known from some regions of RFE, were found for the first time in Amurskaya Oblast: Phyllonorycter populifoliella (Treitschke), Primorskii Krai: Ph. sorbicola Kumata and Sahkalin Island: Caloptilia heringi Kumata, Ph. ermani (Kumata) and Ph. ulmifoliella (Hübner). Eight gracillariid–plant associations are novel to science: Caloptilia gloriosa Kumata on Acer pseudosieboldianum, Cameraria niphonica Kumata on A. caudatum subsp. ukurundense, Parornix ermolaevi Kuznetzov on Corylus sieboldiana, Phyllonorycter ermani (Kumata) on Betula platyphylla, Ph. nipponicella (Issiki) on Quercus mongolica, Ph. orientalis (Kumata) and Ph. pseudojezoniella Noreika on Acer saccharum, Ph. sorbicola on Prunus maakii. For the first time we documented the “green island” phenotype on Phyllonorycter cavella (Zeller) mines on Betula platyphylla. Two pestiferous species have been recorded during our surveys: Micrurapteryx caraganella on ornamental Caragana arborescens in urban plantations in Amurskaya Oblast, and the lime leafminer Phyllonorycter issikii (Kumata), a species known to be native to RFE and invasive elsewhere in Russia and in European countries. A revised checklist of RFE gracillariids has been compiled. It accounts for 135 species among which 17 species (13%) are only known to occur in RFE. The gracillariid fauna of RFE is more similar to the Japanese fauna (49%), than to the fauna of the rest of Russia (i.e European part and Siberia) (32%).
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Pipinis, Elias, Stefanos Hatzilazarou, Stefanos Kostas, Soumaya Bourgou, Wided Megdiche-Ksouri, Zeineb Ghrabi-Gammar, Mohamed Libiad, et al. "Facilitating Conservation and Bridging Gaps for the Sustainable Exploitation of the Tunisian Local Endemic Plant Marrubium aschersonii (Lamiaceae)." Sustainability 14, no. 3 (January 30, 2022): 1637. http://dx.doi.org/10.3390/su14031637.
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In the frame of conservation and sustainable utilization of neglected and underutilized phytogenetic resources, this study produced for the first time a detailed ecological profiling for the local Tunisian endemic Marrubium ascheronii (Lamiaceae) using Geographical Information Systems and open-source data. This profile was used to illustrate the abiotic environmental conditions of its wild habitats; the profile facilitated the examination of the effect of temperature on its seed germination and may inform species-specific guidelines for its cultivation in man-made environments. With effective seed propagation firstly reported herein (68.75% at 20 °C), species-specific in situ conservation efforts and ex situ conservation or sustainable exploitation strategies were enabled for M. aschersonii. The first-reported molecular authentication (DNA barcoding) of M. aschersonii may facilitate its traceability, allowing for product design. This study also reports for the first time the effects of chemical and integrated nutrient management (INM) fertilizers on the growth and pilot cultivation of M. aschersonii seedlings, with the latter being advantageous. This multidisciplinary approach has bridged important research gaps that hindered the conservation efforts and/or the sustainable exploitation for this local endemic plant of Tunisia. Based on all the above, we re-evaluated and updated the feasibility and readiness timescale for sustainable exploitation of M. aschersonii in the medicinal-cosmetic, agro-alimentary and ornamental-horticultural sectors.
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Park, Young Sang, Jong-Soo Kang, Jee Young Park, Hyeonah Shim, Hyun Ok Yang, Jung Hwa Kang, and Tae-Jin Yang. "Analysis of the complete plastomes and nuclear ribosomal DNAs from Euonymus hamiltonianus and its relatives sheds light on their diversity and evolution." PLOS ONE 17, no. 10 (October 5, 2022): e0275590. http://dx.doi.org/10.1371/journal.pone.0275590.
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Euonymus hamiltonianus and its relatives (Celastraceae family) are used for ornamental and medicinal purposes. However, species identification in Euonymus is difficult due to their morphological diversity. Using plastid genome (plastome) data, we attempt to reveal phylogenetic relationship among Euonymus species and develop useful markers for molecular identification. We assembled the plastome and nuclear ribosomal DNA (nrDNA) sequences from five Euonymus lines collected from South Korea: three Euonymus hamiltonianus accessions, E. europaeus, and E. japonicus. We conducted an in-depth comparative analysis using ten plastomes, including other publicly available plastome data for this genus. The genome structures, gene contents, and gene orders were similar in all Euonymus plastomes in this study. Analysis of nucleotide diversity revealed six divergence hotspots in their plastomes. We identified 339 single nucleotide polymorphisms and 293 insertion or deletions among the four E. hamiltonianus plastomes, pointing to abundant diversity even within the same species. Among 77 commonly shared genes, 9 and 33 were identified as conserved genes in the genus Euonymus and E. hamiltonianus, respectively. Phylogenetic analysis based on plastome and nrDNA sequences revealed the overall consensus and relationships between plastomes and nrDNAs. Finally, we developed six barcoding markers and successfully applied them to 31 E. hamiltonianus lines collected from South Korea. Our findings provide the molecular basis for the classification and molecular taxonomic criteria for the genus Euonymus (at least in Korea), which should aid in more objective classification within this genus. Moreover, the newly developed markers will be useful for understanding the species delimitation of E. hamiltonianus and closely related species.
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Fahmi, Melta Rini, Erma Primanita Hayuningtyas, Mochammad Zamroni, Bastiar Nur, and Shofihar Sinansari. "KERAGAMAN GENETIK IKAN TIGER FISH (Datnioides sp.) ASAL KALIMANTAN DAN SUMATERA." Jurnal Riset Akuakultur 13, no. 3 (December 6, 2018): 191. http://dx.doi.org/10.15578/jra.13.3.2018.191-199.
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Ikan tiger fish (Datnioides sp.) merupakan ikan hias air tawar yang memiliki nilai ekonomis penting. Distribusi populasi ikan ini meliputi Papua, Kalimantan, dan Sumatera, dengan tingkat eksploitasi yang cukup tinggi di dua lokasi terakhir. Penelitian ini dilakukan untuk mendapatkan informasi keragaman genetik ikan tiger fish yang mendiami perairan Kalimantan dan Sumatera. Sebanyak 24 sampel ikan uji dikoleksi dari Sungai Kapuas, Kalimantan Barat dan Sungai Musi, Sumatera Selatan. Penelitian dilakukan dalam dua tahap, tahap pertama yaitu identifikasi molekuler dengan menggunakan DNA barcoding gen cytochrome oxidase 1 (COI), tahap kedua adalah analisis keragaman genetik dengan menggunakan marka DNA mitokondria gen cytochrome b (Cyt b), dan DNA inti gen recombination activating gene (RAG2). Hasil identifikasi secara molekuler menunjukkan bahwa ikan hasil koleksi memiliki kesamaan genetik sebesar 100% dengan spesies D. undecimradiatus. Keragaman genetik ikan tiger fish antar populasi berkisar pada nilai 0,023 (standar deviasi 0,001) sedangkan keragaman intra populasi adalah sebesar 0,002 dan 0,003 masing-masing untuk populasi Kalimantan dan Sumatera. Jarak genetik sampel baik yang berasal dari Sumatera maupun Kalimantan dengan spesies D. undeciumradiatus masing-masing 0,003 dan 0,006; sedangkan dengan spesies D. microlepis yaitu 0,142. Analisis menggunakan gen RAG2 menunjukkan sampel yang diuji memiliki struktur populasi yang terpisah ditandai dengan terjadinya mutasi pada enam nukleotida dan tiga asam amino.The Tiger fish (Datnioides sp.) is a freshwater ornamental fish that has important economic value. The distribution of this fish included Papua, Kalimantan, and Sumatra, but intensive exploitation occurs in the last two population. This research was conducted to obtain the genetic diversity of tiger fish that inhabited in Kalimantan and Sumatra. A total of 24 fish were collected from Kapuas River, West Kalimantan and Musi River, at Sumatra. The study was conducted in two stages, the first stage is molecular identification of sample by using DNA barcoding cytochrome oxidase 1 (COI) gene, the second stage is analyses of genetic diversity of tiger fish within and between population by using the mitochondrial DNA cytochrome b (Cyt b) gene, and nucleus DNA recombination (RAG2) gene. The molecular identification has shown that the collected fish has a genetic similarity of 100% with D. undecimradiatus. The genetic diversity of tiger fish between populations is 0.023 (standard deviation of 0.001) whereas intra-population is 0.002 and 0.003 for Kalimantan and Sumatra, respectively. The genetic distance of samples with species D. undeciumradiatus were 0.003 and 0.006 for Kalimantan and Sumatera, respectively, whereas the genetic distance with D. microlepis was 0.142. The analysis of mutation on RAG2 gene shows there are six nucleotides and three amino acids have mutation.
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ABUJAM, SANTOSHKUMAR, LAKPA TAMANG, GIBJI NIMASOW, and DEBANGSHU NARAYAN DAS. "Trade Potential of Indigenous Ornamental Fishes of Arunachal Pradesh, India." Asian Fisheries Science 34, no. 4 (December 31, 2021). http://dx.doi.org/10.33997/j.afs.2021.34.4.004.
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Arunachal Pradesh is rich with networks of drainage systems with enormous wild fish diversity due to varied climatic and topographical features. Most of the streams harbour very alluring small indigenous minnows, loaches, catfishes and barbs that have hardly been exploited for the ornamental fish market. If these aquatic resources are sustainably utilised as a trade commodity, then the pattern of livelihood of the local populace may be uplifted economically. The present investigation was undertaken to establish the market potential of certain indigenous ornamental fishes of Arunachal Pradesh. The survey was conducted during 2019–2020 for 6 months (October–March) based on the feasibility of accessible collections. A total of 52 ornamental fish species under 6 orders and 15 families were documented and collected during the surveys in various streams and rivers. The collection showed that 4 species namely Balitora brucei Gray, 1830, Aborichthys kempi Chaudhuri, 1913, Schistura devdevi Hora, 1935, and Neolissochilus hexagonolepis (McClelland, 1839) were recorded under near threatened; Lepidocephalichthys arunachalensis (Datta & Barman, 1984) and Botia rostrata Günther, 1868, under endangered and vulnerable categories, respectively as per International Union for Conservation of Nature (IUCN) status. The species documented exhibiting natural ornamental features herein considered an indigenous ornamental fish (IOF) for depicting their market demand showing the minimal price of each individual species towards the development of organised trade in Arunachal Pradesh.
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Goswami, Mukunda, A. Pavan-Kumar, Grishma S. Patil, Trinica George, Rupak Nath, R. Bhuyan, C. Siva, M. A. Laskar, and Samson Sumer. "Molecular identification of ornamental loaches (Cypriniformes, Cobitoidei) of North East India using mitochondrial genes." Animal Gene, August 2022, 200136. http://dx.doi.org/10.1016/j.angen.2022.200136.
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KUSMINTARSIH, ENDANG SRIMURNI, HANAN HASSAN ALSHEIKH MAHMOUD, MOH HUSEIN SASTRANEGARA, HAMDAN SYAKURI, AGUS NURYANTO, and TRISNOWATI BUDI AMBARNINGRUM. "Barcoding of ornamental freshwater shrimp, Neocaridina denticulata (De Haan, 1844) from the aquatic ornamental market in Purbalingga, Central Java, Indonesia." Biodiversitas Journal of Biological Diversity 24, no. 7 (July 23, 2023). http://dx.doi.org/10.13057/biodiv/d240714.
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Abstract. Kusmintarsih ES, Mahmoud HHA, Sastranegara MH, Syakuri H,Nuryanto A, Ambarningrum TB. 2023. Barcoding of ornamental freshwater shrimp, Neocaridina denticulata (De Haan, 1844) from the aquatic ornamental market in Purbalingga, Central Java, Indonesia. Biodiversitas 24: 3601-3608. Indonesia is one of the world’s leading aquatic ornamental shrimps producers and exports. One of the aquatic ornament shrimp species is a Neocaridina denticulate (De Haan, 1844). There is a wide range of colors including red, bright red, yellow, orange, green, blue, violet, black, and color combinations. It is a landlocked Atydiae family species comprising31 species and subspecies. Due to taxonomic difficulties, this species is continually under revision, and the validation of a few species is currently questionable and uncertain for the relationships among the various colors of N. denticulata. The Cytochrome Oxidase gene I (CO1) gene sequences of mitochondrial DNA were used for species DNA barcoding studies. This study aimed to validate the taxonomic status of different colors of N. denticulata species using the mitochondrial DNA or mtDNA Cytochrome oxidase (CO1) gene sequences. Neighbour Joining trees were constructed based on 545 bp of CO1 gene from white, black, red, yellow, blue colors, and their combination. Several sequences were derived from GenBank for relevant species from different countries and the outgroup. The result showed that all samples are homolog, even to N. denticulata from China NC_023823.1.
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Hubert, Nicolas, Kadarusman, Arif Wibowo, Frédéric Busson, Domenico Caruso, Sri Sulandari, Nuna Nafiqoh, et al. "DNA Barcoding Indonesian freshwater fishes: challenges and prospects." DNA Barcodes 3, no. 1 (January 1, 2015). http://dx.doi.org/10.1515/dna-2015-0018.
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AbstractWith 1172 native species, the Indonesian ichthyofauna is among the world’s most speciose. Despite that the inventory of the Indonesian ichthyofauna started during the eighteen century, the numerous species descriptions during the last decades highlight that the taxonomic knowledge is still fragmentary. Meanwhile, the fast increase of anthropogenic perturbations during the last decades is posing serious threats to Indonesian biodiversity. Indonesia, however, is one of the major sources of export for the international ornamental trade and home of several species of high value in aquaculture. The development of new tools for species identification is urgently needed to improve the sustainability of the exploitation of the Indonesian ichthyofauna. With the aim to build comprehensive DNA barcode libraries, the co-authors have started a collective effort to DNA barcode all Indonesian freshwater fishes. The aims of this review are: (1) to produce an overview of the ichthyological researches conducted so far in Indonesia, (2) to present an updated checklist of the freshwater fishes reported to date from Indonesia’s inland waters, (3) to highlight the challenges associated with its conservation and management, (4) to present the benefits of developing comprehensive DNA barcode reference libraries for the conservation of the Indonesian ichthyofauna.
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Wiadnya, Dewa Gede Raka, Nia Kurniawan, Anik Martinah Hariati, Septiana Sri Astuti, Akhsan Fikrillah Paricahya, Muhammad Dailami, and Wahyu Endra Kusuma. "DNA barcoding of the most common marine ornamental fish species spilled over from a small-sized marine protected area, Bali Barat National Park, Indonesia." Biodiversitas Journal of Biological Diversity 24, no. 1 (January 18, 2023). http://dx.doi.org/10.13057/biodiv/d240107.
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Abstract. Wiadnya DGR, Kurniawan N, Hariati AM, Astuti SS, Paricahya AF, Dailami M, Kusuma WE. 2023. DNA barcoding of the most common marine ornamental fish species spilled over from a small-sized marine protected area, Bali Barat National Park, Indonesia. Biodiversitas 243: 47-54. Healthy coral reefs within a protected area may function as a source of recruitment to the surroundings through spill-over and export larvae. This study aims to generate a list of common species of marine ornamental fishes for the aquarium trade in Indonesia, mainly collected adjacent to Bali Barat National Park (BBNP). Lived-fish samples were collected from six fish collectors in two villages surrounding BBNP, Sumber Kima, Bali, and Bangsring, Banyuwangi. All species were checked by three active fishermen in both villages for confirmation of the most common species and not belonging to the target. A total of 82 separate groups out of 145 specimens were identified based on their morphological characters. All samples were then sequenced based on mitochondrial cytochrome oxidase subunit I (COI) gene amplification. The sequence read lengths for all the specimens were between 655 and 658 bp. All the findings from this DNA barcoding approach were in line with morphological species identification. Wrasses (Family: Labridae) were the most dominant (41 species) representing the group, followed by Pomacentridae (24 species), Acanthuridae (14 species), Pomacanthidae (14 species) and Gobiidae (10 species). Among the species, only green sergeant, Amblyglyphidodon batunaorum, belonged to the Vulnerable (VU) category based on IUCN criteria. The rest were either Least Concern (LC), Data Deficient (DD), or Not Evaluated (NE). It implied that no catch species were under fishing pressure except for the green sergeant. Considering a total of 28 target species by local fishermen (recorded in an earlier article), small-scale fishermen can easily catch more than 100 species in one trip. The results significantly contributed to the need to generate a list of common ornamental fish species specifically exported from Indonesia as an aquarium trade commodity.
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Aghayeva, Parvin, Salvatore Cozzolino, Donata Cafasso, Valida Ali-zade, Silvia Fineschi, and Dilzara Aghayeva. "DNA barcoding of native Caucasus herbal plants: potentials and limitations in complex groups and implications for phylogeographic patterns." Biodiversity Data Journal 9 (January 27, 2021). http://dx.doi.org/10.3897/bdj.9.e61333.
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DNA barcoding has rapidly become a useful complementary tool in floristic investigations particularly for identifying specimens that lack diagnostic characters. Here, we assess the capability of three DNA barcode markers (chloroplast rpoB, accD and nuclear ITS) for correct species assignment in a floristic survey on the Caucasus. We focused on two herbal groups with potential for ornamental applications, namely orchids and asterids. On these two plant groups, we tested whether our selection of barcode markers allows identification of the “barcoding gap” in sequence identity and to distinguish between monophyletic species when employing distance-based methods. All markers successfully amplified most specimens, but we found that the rate of species-level resolution amongst selected markers largely varied in the two plant groups. Overall, for both lineages, plastid markers had a species-level assignment success rate lower than the nuclear ITS marker. The latter confirmed, in orchids, both the existence of a barcoding gap and that all accessions of the same species clustered together in monophyletic groups. Further, it also allowed the detection of a phylogeographic signal.The ITS marker resulted in its being the best performing barcode for asterids; however, none of the three tested markers showed high discriminatory ability. Even if ITS were revealed as the most promising plant barcode marker, we argue that the ability of this barcode for species assignment is strongly dependent on the evolutionary history of the investigated plant lineage.
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Liu, Yixin, Mingfang Zhang, Xuqing Chen, Xi Chen, Yue Hu, Junlian Gao, Wenqiang Pan, et al. "Developing an efficient DNA barcoding system to differentiate between Lilium species." BMC Plant Biology 21, no. 1 (October 13, 2021). http://dx.doi.org/10.1186/s12870-021-03229-6.
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Abstract Background Lilium is an important ornamental bulb, possesses medicinal properties, and is also edible. Species within the Lilium genus share very similar morphology and macroscopic characteristics, thus they cannot be easily and clearly distinguished from one another. To date, no efficient species-specific markers have been developed for classifying wild lily species, which poses an issue with further characterizing its medicinal properties. Results To develop a simple and reliable identification system for Lilium, 45 representative species from 6 sections were used to develop a DNA barcoding system, which was based on DNA sequence polymorphisms. In this study, we assessed five commonly used DNA barcode candidates (ITS, rbcL, ycf1b, matK and psbA-trnH) and five novel barcode candidates obtained from highly variable chloroplast genomic regions (trnL-trnF, trnS-trnG, trnF-ndhJ, trnP-psaJ-rpI33 and psbB-psbH). We showed that a set of three novel DNA barcodes (ITS + trnP-psaJ-rpI33 + psbB-psbH) could be efficiently used as a genetic marker to distinguish between lily species, as assessed by methods including DNAsp, BI and ML tree, and Pair Wise Group (PWG). Conclusions A rapid and reliable DNA barcoding method was developed for all 45 wild Lilium species by using ITS, trnP-psaJ-rpI33, and psbB-psbH as DNA barcoding markers. The method can be used in the classification of wild Lilium species, especially endangered species, and also provides an effective method for selective lily breeding.
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Patil, Grishma S., Nevil Pinto, Rupak Nath, and Mukunda Goswami. "Decoding the molecular phylogenetics of ornamental catfishes (siluriformes) of North East India using DNA barcoding approach." Molecular Biology Reports 51, no. 1 (April 18, 2024). http://dx.doi.org/10.1007/s11033-024-09487-5.
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Upshur, Irving Forde, Mikhyle Fehlman, Vansh Parikh, Clément Vinauger, and Chloé Lahondère. "Sugar feeding by invasive mosquito species on ornamental and wild plants." Scientific Reports 13, no. 1 (December 13, 2023). http://dx.doi.org/10.1038/s41598-023-48089-2.
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AbstractFeeding on plant-derived sugars is an essential component of mosquito biology, affecting key aspects of their lives such as survival, metabolism, and reproduction. Among mosquitoes, Aedes aegypti and Aedes albopictus are two invasive mosquito species in the US, and are vectors of diseases such as dengue fever, chikungunya, and Zika. These species live in heavily populated, urban areas, where they have high accessibility to human hosts as well as to plants in backyards and public landscapes. However, the range of plants that are suitable sugar hosts for these species remains to be described, despite the importance of understanding what plants may attract or repel mosquitoes to inform citizens and municipal authorities accordingly. Here, we tested whether Ae. aegypti and Ae. albopictus would sugar-feed on eleven commonly planted ornamental plant species. We confirmed feeding activity using the anthrone method and identified the volatile composition of plant headspace using gas-chromatography mass-spectroscopy. These chemical analyses revealed that a broad range of olfactory cues are associated with plants that mosquitoes feed on. This prompted us to use plant DNA barcoding to identify plants that field-caught mosquitoes feed on. Altogether, results show that native and invasive mosquito species can exploit a broader range of plants than originally suspected, including wild and ornamental plants from different phyla throughout the Spring, Summer and Fall seasons.
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Yu, Peng, Li Zhou, Wen-Tao Yang, Li-jun Miao, Zhi Li, Xiao-Juan Zhang, Yang Wang, and Jian-Fang Gui. "Comparative mitogenome analyses uncover mitogenome features and phylogenetic implications of the subfamily Cobitinae." BMC Genomics 22, no. 1 (January 14, 2021). http://dx.doi.org/10.1186/s12864-020-07360-w.
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AbstractBackgroundLoaches of Cobitinae, widely distributed in Eurasian continent, have high economic, ornamental and scientific value. However, the phylogeny of Cobitinae fishes within genera or family level remains complex and controversial. Up to now, about 60 Cobitinae mitogenomes had been deposited in GenBank, but their integrated characteristics were not elaborated.ResultsIn this study, we sequenced and analyzed the complete mitogenomes of a femaleCobits macrostigma. Then we conducted a comparative mitogenome analysis and revealed the conserved and unique characteristics of 58 Cobitinae mitogenomes, includingC. macrostigma. Cobitinae mitogenomes display highly conserved tRNA secondary structure, overlaps and non-coding intergenic spacers. In addition, distinct base compositions were observed among different genus and significantly negative linear correlation between AT% and AT-skew were found among Cobitinae, genusCobitisandPangiomitogenomes, respectively. A specific 3 bp insertion (GCA) in theatp8-atp6overlap was identified as a unique feature of loaches, compared to other Cypriniformes fish. Additionally, all protein coding genes underwent a strong purifying selection. Phylogenetic analysis strongly supported the paraphyly ofCobitisand polyphyly ofMisgurnus. The strict molecular clock predicted that Cobitinae might have split into northern and southern lineages in the late Eocene (42.11 Ma), furthermore, mtDNA introgression might occur (14.40 Ma) between ancestral species ofCobitisand ancestral species ofMisgurnus.ConclusionsThe current study represents the first comparative mitogenomic and phylogenetic analyses within Cobitinae and provides new insights into the mitogenome features and evolution of fishes belonging to the cobitinae family.