Mitochondrial Dna Part a最新文献_第4页

Phylogeny and phylogeography of the genus Alburnoides (Teleostei, Cyprinidae) in Turkey based on mitochondrial DNA sequences 基于线粒体DNA序列的土耳其Alburnoides属(Teleostei, Cyprinidae)的系统发育和系统地理学

4区生物学

Mitochondrial Dna Part a Pub Date : 2019-09-11 DOI: 10.1080/24701394.2019.1664493

Yusuf Bektaş, I. Aksu, C. Kaya, Esra Bayçelebi, Ş. Atasaral, F. G. Ekmekçi, D. Turan

{"title":"Phylogeny and phylogeography of the genus Alburnoides (Teleostei, Cyprinidae) in Turkey based on mitochondrial DNA sequences","authors":"Yusuf Bektaş, I. Aksu, C. Kaya, Esra Bayçelebi, Ş. Atasaral, F. G. Ekmekçi, D. Turan","doi":"10.1080/24701394.2019.1664493","DOIUrl":"https://doi.org/10.1080/24701394.2019.1664493","url":null,"abstract":"Abstract Turkey has a rich freshwater biodiversity in terms of Cyprinid genus in respect to its geographical location. To elucidate the phylogeny of the Alburnoides genus, one of these genera, genetic data for the cytochrome b gene (1141 bp) was generated for 445 samples collected at 42 sampling sites across their geographical distribution. A total of 54 mitochondrial haplotypes identified were distrubuted among distinct twelve species that did not share haplotypes with each other. Pairwise sequence divergence among these species range from 1.37% (A. emineae and A. velioglui) and 10.99% (A. manyasensis and A. smyrnae). A new potential species in the River Dirgine that run into the Black Sea Basin was separated from the most closed known species with mean 6.3%. Network analysis and phylogenetic analysis indicated that all haplotypes were clustered into two major clades, which corresponded to twenty-three Alburnoides lineages, with moderate-high bootstrap supports and mutational steps, respectively. Application of a molecular clock to a Bayesian phylogeny indicates that Alburnoides diversified under the paleogeographic conditions such as tectonic uplift and faulting Miocene aged as well as climatic oscillation and sea-level fluctuations during late Miocene-middle Pleistocene. The genetic results of the present study indicated the inter-specific distance of cyt b gene sequences followed the ideal results for species identification and phylogeny of Turkish spirlins.","PeriodicalId":54298,"journal":{"name":"Mitochondrial Dna Part a","volume":"22 1","pages":"794 - 805"},"PeriodicalIF":0.0,"publicationDate":"2019-09-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"82796799","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 7

Genetic characterization and DNA barcoding of coffee shot-hole borer, Xylosandrus compactus (Eichhoff) (Coleoptera: Curculionidae: Scolytinae) 咖啡针孔虫Xylosandrus compactus (Eichhoff)遗传特征及DNA条形码分析(鞘翅目:锥虫科:锥虫科)

4区生物学

Mitochondrial Dna Part a Pub Date : 2019-09-04 DOI: 10.1080/24701394.2019.1659249

V. S. Kiran, R. Asokan, Revanna Revannavar, Mahadeva Swamy Hanchipura Mallesh, Ellango Ramasamy

{"title":"Genetic characterization and DNA barcoding of coffee shot-hole borer, Xylosandrus compactus (Eichhoff) (Coleoptera: Curculionidae: Scolytinae)","authors":"V. S. Kiran, R. Asokan, Revanna Revannavar, Mahadeva Swamy Hanchipura Mallesh, Ellango Ramasamy","doi":"10.1080/24701394.2019.1659249","DOIUrl":"https://doi.org/10.1080/24701394.2019.1659249","url":null,"abstract":"Abstract Beetles of the subfamily Scolytinae are the most damaging insects in the world. Among which the black twig borer, Xylosandrus compactus (Eichhoff) (Coleoptera: Curculionidae: Scolytinae), is one of the serious pests in coffee plantations. Their cryptic life cycle inside the host plant makes these insects difficult to control. For its effective management accurate, timely and rapid identification of species is critical. By cloning and sequencing the 5' mitochondrial cytochrome oxidase c subunit 1 (COI) gene, the beetle’s molecular identification confirmed its identity as X. compactus. No pseudogenes and indels were found in analyzed nucleotide sequences; they match with high similarity in nucleotide NCBI Basic Local Alignment Search Tool search. The X. compactus COI genes sequences were deposited at NCBI GenBank with accession numbers of KY172634, KY172635 and the Barcode of Life (BOLD) with BIN ID: ACB4177. Furthermore, based on multiple sequence alignment of the X. compactus MtCOI gene, a phylogenetic tree with maximum probability was drawn. X. compactus species clustered together which agree with the species data collected from NCBI GenBank database from the different geographic regions. There were no morphological and molecular differences between space and time—collected coffee shot—hole borers, thus all the specimens described were X. compactus infesting both robusta and arabica coffee.","PeriodicalId":54298,"journal":{"name":"Mitochondrial Dna Part a","volume":"40 1","pages":"779 - 785"},"PeriodicalIF":0.0,"publicationDate":"2019-09-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"86358119","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 3

Novel diversity in mitochondrial genomes of deep-sea Pennatulacea (Cnidaria: Anthozoa: Octocorallia) 深海盘藻目线粒体基因组的新多样性(刺胞目:珊瑚虫目:章鱼目)

4区生物学

Mitochondrial Dna Part a Pub Date : 2019-07-18 DOI: 10.1080/24701394.2019.1634699

R. I. Hogan, K. Hopkins, A. Wheeler, A. Allcock, Chris, Yesson

引用次数: 19

MeDIP-seq reveals the features of mitochondrial genomic methylation in immature testis of Chinese mitten crab Eriocheir sinensis MeDIP-seq揭示中华绒螯蟹未成熟睾丸线粒体基因组甲基化特征

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Mitochondrial Dna Part a Pub Date : 2018-04-01 DOI: 10.1080/24701394.2016.1278537

Gen-Liang Li, Yi-Jiao Xu, Xiaomin Huang, Juan Xiao, Song Nong, Chao-gan Li

引用次数: 3

Mitogenomic analysis in European brown hare (Lepus europaeus) proposes genetic and functional differentiation between the distinct lineages 欧洲褐兔(Lepus europaeus)的有丝分裂基因组分析提出了不同谱系之间的遗传和功能分化

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Mitochondrial Dna Part a Pub Date : 2018-04-01 DOI: 10.1080/24701394.2016.1278540

T. Giannoulis, C. Stamatis, Andreas Tsipourlianos, Z. Mamuris

{"title":"Mitogenomic analysis in European brown hare (Lepus europaeus) proposes genetic and functional differentiation between the distinct lineages","authors":"T. Giannoulis, C. Stamatis, Andreas Tsipourlianos, Z. Mamuris","doi":"10.1080/24701394.2016.1278540","DOIUrl":"https://doi.org/10.1080/24701394.2016.1278540","url":null,"abstract":"Abstract European brown hare is a small game species spreading across Europe to Asia Minor, with important economic traits. Population genetics studies using mitochondrial DNA markers have revealed the existence of two major phylogeographic lineages, the European and the Anatolian. European lineage is further divided in the European type halpogroup and south-eastern European type halpogroup, while Anatolian consists only by the Anatolian/Middle Eastern type halpogroup. All three haplogroups show a discrete geographical distribution, with an overlapping zone forming in North-East Greece and Bulgaria, forming a contact zone. Despite the existence of a contact zone, European haplotype was never detected in Anatolia and vice versa, proposing the presence of genetic barriers responsible for this phenomenon. In this study, we analyzed the whole mitochondrial genomes of specimens originating from both lineages, aiming to detect the genetic and functional differentiation of the oxidative phosphorylation complexes that are encoded by mtDNA that could lead gradually to the reproductive isolation of the lineages.","PeriodicalId":54298,"journal":{"name":"Mitochondrial Dna Part a","volume":"2 1","pages":"353 - 360"},"PeriodicalIF":0.0,"publicationDate":"2018-04-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"83809908","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 14

Back from the dead! Resurrection and revalidation of the Indian endemic snake genus Wallophis Werner, 1929 (Squamata: Colubridae) insights from molecular data 死而复生!印度特有蛇属Wallophis Werner的复活和重新验证，1929(鳞目:蛇科)从分子数据的见解

4区生物学

Mitochondrial Dna Part a Pub Date : 2018-04-01 DOI: 10.1080/24701394.2016.1278536

Z. Mirza, Harshil Patel

引用次数: 11

Identification of traditional Chinese medicinal pipefish and exclusion of common adulterants by multiplex PCR based on 12S sequences of specific alleles 基于特异等位基因12S序列的多重PCR鉴定中药管鱼及常见掺假物的排除

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Mitochondrial Dna Part a Pub Date : 2018-04-01 DOI: 10.1080/24701394.2016.1278538

Linhui Gao, Yan Yin, Jia Li, Yuan Yuan, Chao Jiang, Wei Gao, Xia-nan Zhang, Luqi Huang

{"title":"Identification of traditional Chinese medicinal pipefish and exclusion of common adulterants by multiplex PCR based on 12S sequences of specific alleles","authors":"Linhui Gao, Yan Yin, Jia Li, Yuan Yuan, Chao Jiang, Wei Gao, Xia-nan Zhang, Luqi Huang","doi":"10.1080/24701394.2016.1278538","DOIUrl":"https://doi.org/10.1080/24701394.2016.1278538","url":null,"abstract":"Abstract We aimed to establish a rapid and accurate allele-specific diagnostic Polymerase Chain Reaction (PCR) method for medicinal pipefish. To achieve this, pipefish genomic DNA was extracted, sequenced bi-directionally, and the data were analyzed. On this basis, specific identification primers were designed and a facile multiplex PCR system was established and optimized. Phylogenetic tree analysis showed that the six species of pipefish were strictly clustered in separate single branches. The reaction was optimized for ease of application, to be used in a reaction volume of 20 μL with template DNA amounts in the range of 5–100 ng, and an annealing temperature from 43 to 55 °C. The reactions conducted using authentic samples of Syngnathoides biaculeatus, Solenognathus hardwickii, and Syngnathus acus produced clear single DNA bands of 240 bp, 318 bp, and 139 bp, respectively. The observed amplicons correspond very well to the specific identification primers HLN, HLD, HLJ, as designed. Thus, it can be concluded that our identification system is specific and stable, and can be used to quickly and accurately identify complex multi-source pipefish samples. We hope that the system will not only ensure the quality of traditional Chinese medicinal ingredients, but also help conservation efforts by offering a quick and easy identification method for pipefish.","PeriodicalId":54298,"journal":{"name":"Mitochondrial Dna Part a","volume":"365 1","pages":"340 - 346"},"PeriodicalIF":0.0,"publicationDate":"2018-04-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"77327181","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 7

Functional, structural, and phylogenetic analysis of mitochondrial cytochrome b (cytb) in insects 昆虫线粒体细胞色素b (cytb)的功能、结构和系统发育分析

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Mitochondrial Dna Part a Pub Date : 2018-02-17 DOI: 10.1080/24701394.2016.1275596

S. Seddigh, M. Darabi

{"title":"Functional, structural, and phylogenetic analysis of mitochondrial cytochrome b (cytb) in insects","authors":"S. Seddigh, M. Darabi","doi":"10.1080/24701394.2016.1275596","DOIUrl":"https://doi.org/10.1080/24701394.2016.1275596","url":null,"abstract":"Abstract Cytochrome b (Cytb, EC 1.10. 2.2) is the only cytochrome coded by mitochondrial DNA and involved in electron transport in the mitochondrial respiratory chain. In this study, characterization of cytb protein was identified on fifty-four insect protein sequences, from different orders. According to the conserved motifs obtained with MEME and MAST tools, eight motifs were common to all insects. The structural and functional analyses of 16 selected insects from different orders were performed with ProtParam, Compute PI, SOPMA, SignalP 4.1, TMHMM 2.0, ProtScale and ProDom tools in the ExPASy database and DNASTAR 12.1 software. The tertiary structure of Drosophila melanogaster as a sample of insects was predicted by the Phyre2 and TM-score servers and their similarities were verified by SuperPose servers. The tertiary structures were predicted using the ‘d1ppjc2’ model (PDB accession code: 1ppj C). A phylogenetic tree was constructed with MEGA 6.06 software using the neighbour-joining method. According to the results, there is a high identity of cytb in different insects so that they should be derived from a common ancestor. In protein–protein interaction analysis with STRING 10.0, twenty-three enriched pathways of KEGG were identified in D. melanogaster and other species. The obtained data provided a background for bioinformatic studies of the function and evolution of other insects and organisms.","PeriodicalId":54298,"journal":{"name":"Mitochondrial Dna Part a","volume":"40 1","pages":"236 - 249"},"PeriodicalIF":0.0,"publicationDate":"2018-02-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"87643679","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 12

Genetic diversity and relationship of Indian Muscovy duck populations 印度番鸭种群的遗传多样性及亲缘关系

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Mitochondrial Dna Part a Pub Date : 2018-02-17 DOI: 10.1080/24701394.2016.1261851

Paramasivam Kameshpandian, Subhash Thomas, M. Nagarajan

引用次数: 6

Phylogeography of freshwater fish Puntius sophore in India 印度淡水鱼的系统地理学

4区生物学

Mitochondrial Dna Part a Pub Date : 2018-02-17 DOI: 10.1080/24701394.2016.1275598

R. K. Negi, B. Joshi, J. Johnson, Rahul De, S. Goyal

{"title":"Phylogeography of freshwater fish Puntius sophore in India","authors":"R. K. Negi, B. Joshi, J. Johnson, Rahul De, S. Goyal","doi":"10.1080/24701394.2016.1275598","DOIUrl":"https://doi.org/10.1080/24701394.2016.1275598","url":null,"abstract":"Abstract Phylogeography and evolutionary history of the freshwater species are poorly known. We document the phylogeography of widely distributed Puntius sophore using cytochrome oxidase subunit I (COI) gene of 650 bp. In the present study, we used 61 individual sequences from known geographic locations across India whereas data are lacking from other parts of its distribution range. Total 20 haplotypes with the intra-species sequence divergence ranging from 0.004 to 0.025 were observed and they were split into two major clades (North and Northeastern to Central India). Two distant geographic (North and Northeastern to Central India) regions shared haplotype suggesting ancient river connectivity or introduction of species from Northeast and Central India. Overall nucleotide and haplotype diversities were 0.00971 and 0.915. The Tajima’s D and Fu’s Fs values were found negative but non-significant thus rejecting the population expansion model followed by the multimodal mode of mismatch distribution. Bayesian skyline plots from both the clade showed steady population history over time; and start of decline in recent years in the clade B (∼1000–1500 years). The present finding is in support to the ‘Satpura hypothesis’ proposed to explain species movement patterns from Southeast Asian countries to Indian subcontinent, seconded by P. sophore showing high genetic diversity within Northern India clade (high genetic splits) because of presence of high river network in comparison to other parts of the country.","PeriodicalId":54298,"journal":{"name":"Mitochondrial Dna Part a","volume":"14 1","pages":"256 - 265"},"PeriodicalIF":0.0,"publicationDate":"2018-02-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"90920829","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 8