Academic literature on the topic 'Mt-COI'
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Journal articles on the topic "Mt-COI"
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KALAWATE, APARNA SURESHCHANDRA, K. P. DINESH, and A. SHABNAM. "DNA barcoding unravels three new species and a subspecies of Olepa Watson, 1980 (Lepidoptera, Erebidae, Arctiinae) from India, with morphotypes." Journal of Insect Biodiversity 19, no. 2 (September 30, 2020): 44–60. http://dx.doi.org/10.12976/jib/2020.19.2.2.
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The genus Olepa is distributed in Palearctic and Oriental regions with more species in India and Sri Lanka. In the recent studies, morphological variations within the group were well established, with couple of first set of mt COI DNA barcodes for at least three species. In the present account, three new species and a new subspecies are described from the northern Western Ghats region of Maharashtra based on mt COI DNA barcode studies. Due to high morphological divergence and complete genetic homogeneity on the mt COI DNA, four morphotypes under two species are reported. Morphological and genital characters of male and female are provided along with their respective species morphotypes for the first time under this genus from India. The genitalia and the habitus of male and female are illustrated. Preliminary phylogenetic tree based on the mt COI DNA sequences available in the GenBank for the genus with the sequences for the new species also provided and discussed. Key words: new taxa, morphotype, Maharashtra, DNA barcoding, mt COI gene
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Wallace, LaShanale, Sharifeh Mehrabi, Methode Bacanamwo, Xuebiao Yao, and Felix O. Aikhionbare. "Expression of mitochondrial genes MT-ND1, MT-ND6, MT-CYB, MT-COI, MT-ATP6, and 12S/MT-RNR1 in colorectal adenopolyps." Tumor Biology 37, no. 9 (June 22, 2016): 12465–75. http://dx.doi.org/10.1007/s13277-016-5101-3.
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Fang, Yiliang, Jianqing Zhang, Rongquan Wu, Baohai Xue, Qianqian Qian, and Bo Gao. "Genetic Polymorphism Study on Aedes albopictus of Different Geographical Regions Based on DNA Barcoding." BioMed Research International 2018 (May 29, 2018): 1–10. http://dx.doi.org/10.1155/2018/1501430.
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Aedes albopictus is a very important vector for pathogens of many infectious diseases including dengue fever. In this study, we explored the genetic polymorphism of Aedes albopictus strains in different geographical regions using DNA barcoding of mitochondrial COI (MT-COI) gene. We collected MT-COI sequence of 106 Aedes albopictus mosquitos from 6 provinces in China including Fujian, Guangdong, Hainan, Yunnan, and Taiwan. The length of the sequences is 709bp with the content of A+T (67.7%) greater than that of G+C (32.3%). We identified mutations in 90 (13.68%) loci, of which 57 (63.33%) are transitions, 28 (31.11%) are transversions, and 5 (5.56%) are hypervariable loci. In addition, we obtained 42 haplotypes, 4 (9.52%) of which are shared among different populations. The haplotype diversity of Aedes albopictus is 0.882 and nucleotide diversity is 0.01017. Moreover, the pedigree network diagram shows that most haplotypes are under parallel evolution, suggesting a local expansion of Aedes albopictus in history. Finally, the Neighbor-Joining tree of MT-COI haplotypes reveals a certain correlation between haplotype clusters and geographical distribution, and there are differences among Aedes albopictus in different geographical regions. In conclusion, DNA barcoding of MT-COI gene is an effective method to study the genetic structure of Aedes albopictus.
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Kalawate, Aparna Sureshchandra, Shital Pawara, A. Shabnam, and K.P. Dinesh. "DNA barcode reveals the occurrence of Palearctic Olepa schleini Witt et al., 2005 (Lepidoptera: Erebidae: Arctiinae) from peninsular India with morphological variations and a new subspecies." Journal of Threatened Taxa 12, no. 9 (June 26, 2020): 16143–52. http://dx.doi.org/10.11609/jott.5596.12.9.16143-16152.
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The present study was taken up to report a new record of the tiger moth genus, Olepa Watson, 1980 from India along with the discovery of a new subspecies. Earlier the genus was thought to have restricted distribution range in South and South-East Asia until the report of O. schleini Witt, Müller, Kravchenko, Miller, Hausmann & Speidel from the Mediterranean Coastal Plain of Israel in 2005. The species identification and the new subspecies is proposed based on the combination of morphological studies, available literature comparisons, geographical distribution, DNA barcoding and its phylogeny. Morphological character crypticity and genital structure variations are well documented in the genus with ‘bio-species’ groups. DNA Barcoding data of mt COI has provided some resolution in sorting the problems of ‘bio-species’ groups of the genus in the past studies. In the present study, with the available mt DNA COI barcodes and newly generated barcodes genetic identity is confirmed for the species O. ricini, O. schleini, O. toulgoeti and Olepa schleini chandrai ssp. nov., with their phylogenetic relationships. Morphological variations within the O. schleini species complex are discussed with a new record of the species for India and a new subspecies description. With the first mt COI barcode phylogeny for the genus, comments are made on the taxonomic identity of the mt COI DNA barcodes available in the GenBank for the Olepa species from India.
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Pan, Zhao, Jia-Chong Duan, Qi Gao, and Daniel K. Young. "The Adult, Larva, and Pupa of a New Pseudopyrochroa (Coleoptera: Pyrochroidae: Pyrochroinae) from China, with Molecular Phylogenetic Inferences." Insects 12, no. 12 (December 4, 2021): 1089. http://dx.doi.org/10.3390/insects12121089.
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A new species of Pseudopyrochroa Pic, 1906, P. reni Pan & Young, n. sp., is described from the western region of Mt. Qinling, China. Larvae, pupae, and adults were associated using molecular phylogenetic analyses based on mtDNA COI barcode sequences. All three stages are described and illustrated. Additionally, preliminary phylogenetic relationships among five genera and 14 species of Pyrochroidae, including Pseudopyrochroa, are hypothesized based on COI sequence data. The fauna of Pyrochroidae from the Mt. Qinling biodiversity conservation area is discussed.
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Kamal, Mohammad Mukhlis, Agus Alim Hakim, Nurlisa Alias Butet, Yulia Fitrianingsih, and Rika Astuti. "AUTENTIKASI SPESIES IKAN KERAPU BERDASARKAN MARKA GEN MT-COI DARI PERAIRAN PEUKAN BADA, ACEH." Jurnal Biologi Tropis 19, no. 2 (August 14, 2019): 116. http://dx.doi.org/10.29303/jbt.v19i2.1245.
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Abstrak : Variasi bentuk dan pola pewarnaan tubuh ikan kerapu (Famili Serranidae) sangat variatif, sehingga pengenalan spesies secara morfologis sering tidak akurat. Penelitian ini bertujuan untuk mengautentikasi ikan kerapu dengan menggunakan marka gen COI. Contoh ikan kerapu yang diamati berjumlah 29 ekor yang dikumpulkan dari tiga tempat pendaratan ikan di Perairan Peukan Bada, Propinsi Aceh. Secara karakter morfologis, ikan kerapu tersebut teridentifikasi lebih dari 8 spesies. Untuk analisis DNA, sebanyak 30 mg daging sirip dari setiap ikan contoh diambil untuk dilakukan isolasi dan ekstraksi DNA, kemudian visualisasi elektroforesis dan fragmentasi DNA gen COI dengan metode PCR-sekuensing. Setelah diekstraksi, diperoleh 20 sampel DNA yang tervisualisasi dengan baik, yang dari jumlah tersebut terdapat 16 sampel dapat diamplifikasi. Hasilnya menunjukkan terdapat 6 spesies yang terautentikasi. Kelompok pertama adalah Variola albimarginata, Cephalopholis urodeta, dan C. sexmaculata dengan tingkat kemiripan ≥ 97%. Berikutnya C. boenak, Epinephelus merra, dan Scolopsis vosmeri tingkat kemiripannya ≤ 97%. Bila dibandingkan hasil autentikasi DNA, hasil penelitian menunjukkan bahwa 13 sampel atau > 80% tidak teridentifikasi dengan benar secara morfologis. Berdasarkan jarak genetik, pohon filogeni membentuk 2 clade antara Serranidae dan Nemipteridae. Hasil penelitian menunjukkan bahwa penggunaan marka gen COI sangat efektif untuk autentikasi spesies yang dapat dijadikan sebagai instrumen dalam pemanfaatan dan pengelolaan ikan kerapu.Kata kunci : kerapu, variasi morfologi, gen MT-COI, autentikasi.Abstract : The groupers (family Serranidae) show high variability both in body shapes and coloration leads to highly morphological-based misidentification. The research was aimed in autenthication of the grouper species using MT-COI gene. A total of 29 grouper fishes were collected from three fish landing sites of Peukan Bada, Aceh Province. These fishes were morphologically identified from which more than 8 species were obtained. A 30 mg of the fin meat of each sample was taken for DNA extraction, isolation, electrophoresis visualization, and DNA fragmentation of COI gene using PCR-sequenching. There were 20 DNA samples was clearly visualized of which 16 has been proceeded for amplification. The results showed that V. albimarginata, C. urodeta, and C. sexmaculata showed ≥ 97% similarity, whereas C. boenak, E. merra, dan S. vosmeri with ≤ 97% similarity. Based on phylogenetic tree analysis there was 2 clearly different clades separating family of Serranidae and Nemipteridae. The use of MT-COI gene was effective and accurate tool in species authentication which could be used as an instrument for utilization and management of the grouper species.Keywords : groupers, morphological variation, MT-COI gene, autenthication.
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Cieniewicz, Elizabeth, Victoria Poplaski, Melina Brunelli, Jason Dombroskie, and Marc Fuchs. "Two Distinct Genotypes of Spissistilus festinus (Say, 1830) (Hemiptera, Membracidae) in the United States Revealed by Phylogenetic and Morphological Analyses." Insects 11, no. 2 (January 23, 2020): 80. http://dx.doi.org/10.3390/insects11020080.
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Spissistilus festinus (Say, 1830) (Hemiptera: Membracidae) is a frequent pest of leguminous crops in the Southern United States, and a vector of grapevine red blotch virus. There is currently no information on the genetic diversity of S. festinus. In this study, populations of S. festinus were collected in 2015–2017 from various crops and geographic locations in the United States, and fragments of the mitochondrial cytochrome C oxidase 1 (mt-COI) gene and the nuclear internal transcribed spacer 2 (ITS2) region were characterized by polymerase chain reaction and sequencing. Maximum-likelihood and Bayesian analyses of the mt-COI and ITS2 sequences yielded similar phylogenetic tree topologies, revealing two distinct genetic S. festinus lineages with all of the specimens from California comprising one phylogenetic clade, alongside a single GenBank entry from Arizona, and all specimens from the Southeastern United States comprising a statistically-supported distinct clade, regardless of host and year of collection. The mt-COI gene fragment showed up to 10.8% genetic distance between the two phylogenetic clades. These results suggest the existence of two genotypes within S. festinus in the United States. The only distinct morphological trait between the two genotypes was a less elevated pronotum in the representative specimens from California, compared to the representative specimens from the Southeastern United States. Since this phenotypic feature is inconspicuous, a diagnostic polymerase chain reaction targeting a variable region of the mt-COI fragment was developed to reliably distinguish between the specimens of the two genotypes of S. festinus and to facilitate their specific identification.
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Kurniawaty, Nia, Purnama Hidayat, and Aunu Rauf. "Characterization of Three Species of Thrips on Weeping Fig, Nutmeg, and Marine Seruni Plants Based on Mtcoi DNA Sequences." Biosaintifika: Journal of Biology & Biology Education 8, no. 2 (September 19, 2016): 185. http://dx.doi.org/10.15294/biosaintifika.v8i2.5448.
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<p>Thrips are widely reported as pests in vegetable crops. However, the existence of Phlaeothripidae members has a less concern in Indonesia. Phlaeothripidae is the only family of Tubulifera Suborder and some reports suggested that they had potential to be pests in several crops due to their ability to roll up and to make galls on leaves. The first step in pest management attempt is to identify the pest accurately and quickly, so the pest management can be on target and more efficient. One of the identification methods is the molecular identification using DNA barcoding techniques. This study aimed to characterize and to compare species thrips in banyan, nutmeg, and marine seruni based on their molecular characteristics. This research was conducted in Bogor and Kuningan. The process of molecular characterization consisteds of four steps DNA total extraction, amplification by using PCR, COI gene sequence, and data analysis. PCR programme was succesfully to amplified mt<em>COI</em> gene fragment at 710 bp. The length of mt<em>COI </em>gene of <em>Gynaikothrips uzeli, Haplothrips ganglbaueri</em>, and <em>Pseudophilothrips ichini</em> were 704, 686, and 702 bp dominated by A and T bases with nucleotide variation value of 27.8%. This results confirmed that molecular characterization using mt<em>COI </em>gene mitochondrial had successfully supported the morphological data. </p><p><strong>How to Cite</strong></p><p>Kurniawaty, N., Hidayat, P. & Rauf, A. (2016). Characterization of Three Species of Thrips on Banyan, Nutmeg, and Marine Seruni Plants Based on Coi Gene. <em>Biosaintifika: Journal of Biology & Biology Education</em>, 8(2), 185-192.</p>
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Kholilah, Nenik, Norma Afiati, Subagiyo Subagiyo, and Retno Hartati. "Meta-analysis of Indonesian Octopus laqueus Kaneko & Kubodera 2005 (Cephalopoda: Octopodidae) using Mt-DNA COI as Genetic Marker." Jurnal Kelautan Tropis 24, no. 1 (February 12, 2021): 7–14. http://dx.doi.org/10.14710/jkt.v24i1.10190.
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O. laqueus was first discovered not long ago in 2005 in the Ryuku Islands, Japan. Its geographical distribution and molecular identification are therefore still rarely. Nucleotide sequences based on mt-DNA COI for O. laqueus that have been uploaded in the GenBank until before this study was carried out were only six sequences. Since DNA barcoding of mt-DNA COI has some advantageous characteristics, this study aimed to analyse the genetic difference of Indonesian O. laqueus to the data available in the GenBank. Samples were collected in 2019 - 2020 from Karimunjawa (n=16) and Bangka-Belitung (n=2). The mt-DNA COI was extracted using 10% chelex methods, PCR amplified using Folmer’s primer and sequenced in Sanger methods. Pairwise alignment and genetic distance were carried out in MEGA-X, whereas the phylogenetic tree was reconstructed using Bayesian methods. BLAST identification resulted in 685 bp with a range of 92,07-99,24 percentages of identity. The genetic mean pair-wise distances within-clade were 0,002 and 0,006, whilst the distance between the clade was 0.0883. Combining the suggestion with the ITF current, it is concluded that O. laqueus taken from Karimunjawa raised from the same species as those in Malaysia (MN711655) and Japan (AB302176). Specimens from Bangka-Belitung were suggested came from different species, as they were separated into the second clade by 8.83%. One single sample from Japan (AB430543) which laid outside the two clades by 11.63%-11.38% was also suggested to represent a different species. Overall, this study opens to various further studies on O. laqueus using other loci of genetic markers.
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Beagley, C. Timothy, Ronald Okimoto, and David R. Wolstenholme. "The Mitochondrial Genome of the Sea Anemone Metridium senile (Cnidaria): Introns, a Paucity of tRNA Genes, and a Near-Standard Genetic Code." Genetics 148, no. 3 (March 1, 1998): 1091–108. http://dx.doi.org/10.1093/genetics/148.3.1091.
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Abstract The circular, 17,443 nucleotide-pair mitochondrial (mt) DNA molecule of the sea anemone, Metridium senile (class Anthozoa, phylum Cnidaria) is presented. This molecule contains genes for 13 energy pathway proteins and two ribosomal (r) RNAs but, relative to other metazoan mtDNAs, has two unique features: only two transfer RNAs (tRNAf-Met and tRNATrp) are encoded, and the cytochrome c oxidase subunit I (COI) and NADH dehydrogenase subunit 5 (ND5) genes each include a group I intron. The COI intron encodes a putative homing endonuclease, and the ND5 intron contains the molecule's ND1 and ND3 genes. Most of the unusual characteristics of other metazoan mtDNAs are not found in M. senile mtDNA: unorthodox translation initiation codons and partial translation termination codons are absent, the use of TGA to specify tryptophan is the only genetic code modification, and both encoded tRNAs have primary and secondary structures closely resembling those of standard tRNAs. Also, with regard to size and secondary structure potential, the mt-s-rRNA and mt-l-rRNA have the least deviation from Escherichia coli 16S and 23S rRNAs of all known metazoan mt-rRNAs. These observations indicate that most of the genetic variations previously reported in metazoan mtDNAs developed after Cnidaria diverged from the common ancestral line of all other Metazoa.
Dissertations / Theses on the topic "Mt-COI"
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DIODATO, DARIA. "Identification and functional validation of new mtDNA and nuclear gene variants responsible for mitochondrial disorders." Doctoral thesis, Università degli Studi di Milano-Bicocca, 2014. http://hdl.handle.net/10281/50549.
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My project has been focused on the identification and validation of new mitochondrial gene variants and new mitochondria-related genes.
The first report is about a woman presenting with a stroke-like episode and an history of severe hearing loss, frequent migraines, exercise intolerance, myalgias and limb-girdle muscle weakness indicating a slowly progressive myopathy and secondary amenorrhea with low gonadotropin levels. A muscle biopsy showed ragged-red, cytochrome c oxidase-negative fibers, and an isolated defect of cytochrome c oxidase activity in muscle mitochondria and sequence analysis of muscle mtDNA revealed a new heteroplasmic m.6597C>A transversion in the MTCOI gene, encoding subunit I of cytochrome c oxidase. Analysis on transmitochondrial cybrids demonstrated that the mutation is indeed associated with COX deficiency, i.e. pathogenic.
The second report is about a new phenotype associated to mutations in the AARS2 gene encoding for the mitochondrial aminoacyl tRNA synthetase, identified in six patients presenting with primary ovarian failure, cerebellar and pyramidal signs and cognitive or behavioural disturbances. Two patients underlined a muscle biopsy which showed a severe complex IV defect at histochemical and biochemical analyses.
The third report is about the clinical and biochemical phenotypes associated with mutations in two new mitochondrial aminoacyl tRNA synthetases (ARSs2) genes. In the first patient, an 8 years old child presenting with psychomotor delay, seizures, facial dysmorphisms and hyperlactacidemia and a brain MRI showing hyperintense lesions in the insula and fronto-temporal right cortex, whole exome sequencing (WES) identified a homozygous missense mutation in VARS2, encoding the mitochondrial valyl tRNA-synthetase. In two siblings presenting with a phenotype characterized by hypotonia and psychomotor retardation, high plasma and liquor lactate, both died at few months of age WES revealed two variants in TARS2, encoding the mitochondrial threonyl tRNA-synthetase: a missense and a splice site mutation. VARS2 and TARS2 mutations segregate within patients families. Patients’ clinical- biochemical phenotype and in silico and in vitro analyses of VARS2 and TARS2 mutations clearly indicate these genes as disease-causative. Expression of the corresponding wild-type enzymes led to recovery of the biochemical impairment of mitochondrial respiration in immortalized mutant fibroblasts; yeast modelling of the VARS2 mutation confirmed its pathogenic role.
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Brett, Christy Donna. "Testing the effectiveness of the mt DNA Cytochrome c oxidase subunit 1 (COI) gene locus for identifying species of Polychaete worm (Polychaeta: Annelida) in New Zealand." The University of Waikato, 2006. http://hdl.handle.net/10289/2425.
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The ability to accurately identify species is fundamental to ecological research and environmental monitoring. Current taxonomic identifications often rely on differentiation of morphologically ambiguous characters, and a process of categorization which is tedious and often leads to misidentifications. This is compounded by the presence of cryptic taxa, which may be prevalent among Polychaete worms (Polychaeta: Annelida). With increased access to genetic techniques, Cytochrome c oxidase subunit I has been suggested as a possible aid to assist in the discrimination of species resources. In this study, I tested the hypothesis that the mtDNA COI gene locus is effective in discriminating morphologically recognised species of Polychaete worms. A 543 base-pair fragment of the COI locus was successfully extracted for 111 individuals from 16 out of 20 morphologically recognised species. Average intraspecific divergences were 0.8 %, ranging from 0 % to 5 %. Average interspecific variation was 26.4 %, ranging from 13.8 % to 36.8 %. The lowest divergences were found between two Nereid species (13.8 %), and two Glycera americana species (17.2 %). Relatively high maximum divergences of over 30 % suggest that some species may have reached a divergence saturation level, which may partially explain why familial groupings in constructed trees were not monophyletic. Divergences within the different Nereid species - a group previously known to have morphologically cryptic species - did not reveal the presence of any cryptic taxa. Pairwise comparisons showed a clear divide between percentages of intra- and interspecific divergences, and the suggested threshold of 11 % is effective for the taxa investigated here. On the basis of these results, I conclude that sequence variation in the mtDNA COI gene locus is effective in discriminating morphologically recognised species of Polychaete worms, but may not be appropriate for deeper (e.g. generic or familial) phylogenetic relationships among taxa.