Pub Date : 2019-09-11DOI: 10.1080/24701394.2019.1664493
Yusuf Bektaş, I. Aksu, C. Kaya, Esra Bayçelebi, Ş. Atasaral, F. G. Ekmekçi, D. Turan
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.
{"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}
Pub Date : 2019-09-04DOI: 10.1080/24701394.2019.1659249
V. S. Kiran, R. Asokan, Revanna Revannavar, Mahadeva Swamy Hanchipura Mallesh, Ellango Ramasamy
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.
摘要虫科甲虫是世界上危害最大的昆虫。其中黑枝螟Xylosandrus compactus (Eichhoff)(鞘翅目:曲蝇科:鞘翅科)是咖啡种植园的严重害虫之一。它们在寄主植物内的隐秘生命周期使这些昆虫难以控制。对其进行有效管理，准确、及时、快速的物种鉴定至关重要。通过对该甲虫5'线粒体细胞色素氧化酶c亚基1 (COI)基因的克隆和测序，证实了其分子鉴定为X. compactus。分析的核苷酸序列中未发现假基因和假序列;它们在核苷酸NCBI基本局部比对搜索工具中具有较高的匹配度。该基因序列保存在NCBI GenBank, accession number为KY172634、KY172635, Barcode of Life (BOLD)， BIN ID为ACB4177。在此基础上，基于多序列比对，绘制了具有最大概率的系统发育树。在NCBI GenBank数据库中收集到的不同地理区域的物种数据与紧实X. compactus物种聚类一致。空间和时间采集的咖啡孔螟在形态和分子上没有差异，因此所描述的所有标本都是既侵染罗布斯塔咖啡又侵染阿拉比卡咖啡的紧凑X. compactus。
{"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}
Pub Date : 2019-07-18DOI: 10.1080/24701394.2019.1634699
R. I. Hogan, K. Hopkins, A. Wheeler, A. Allcock, Chris, Yesson
Abstract We present the first documented complete mitogenomes of deep-sea Pennatulacea, representing nine genera and eight families. These include one species each of the deep-sea genera Funiculina, Halipteris, Protoptilum and Distichoptilum, four species each of Umbellula and Pennatula, three species of Kophobelemnon and two species of Anthoptilum, as well as one species of the epi- and mesobenthic genus Virgularia. Seventeen circular genomes ranged from 18,513 bp (Halipteris cf. finmarchica) to 19,171 bp (Distichoptilum gracile) and contained all genes standard to octocoral mitochondrial genomes (14 protein-coding genes, two ribosomal RNA genes and one transfer RNA). We found at least three different gene orders in Pennatulacea: the ancestral gene order, the gene order found in bamboo corals (Family Isididae), and a novel gene order. The mitogenome of one species of Umbellula has a bipartite genome (∼13 kbp and ∼5 kbp), with good evidence that both parts are circular.
摘要本文报道了深海盘藻属(Pennatulacea) 8科9属的完整有丝分裂基因组。这些物种包括深海的Funiculina、Halipteris、Protoptilum和Distichoptilum各一种，umellula和Pennatula各四种，Kophobelemnon三种，Anthoptilum两种，以及外生和中底生的Virgularia一种。17个圆形基因组的长度从18513 bp (haalipteris cf. finmarchica)到19171 bp (Distichoptilum gracile)不等，包含了八珊瑚线粒体基因组的所有标准基因(14个蛋白质编码基因、2个核糖体RNA基因和1个转移RNA)。我们在盘藻中发现了至少三个不同的基因序列:祖先基因序列、竹珊瑚(竹珊瑚科)基因序列和一个新的基因序列。一种伞形植物的有丝分裂基因组具有两部分基因组(~ 13 kbp和~ 5 kbp)，有充分证据表明这两部分都是圆形的。
{"title":"Novel diversity in mitochondrial genomes of deep-sea Pennatulacea (Cnidaria: Anthozoa: Octocorallia)","authors":"R. I. Hogan, K. Hopkins, A. Wheeler, A. Allcock, Chris, Yesson","doi":"10.1080/24701394.2019.1634699","DOIUrl":"https://doi.org/10.1080/24701394.2019.1634699","url":null,"abstract":"Abstract We present the first documented complete mitogenomes of deep-sea Pennatulacea, representing nine genera and eight families. These include one species each of the deep-sea genera Funiculina, Halipteris, Protoptilum and Distichoptilum, four species each of Umbellula and Pennatula, three species of Kophobelemnon and two species of Anthoptilum, as well as one species of the epi- and mesobenthic genus Virgularia. Seventeen circular genomes ranged from 18,513 bp (Halipteris cf. finmarchica) to 19,171 bp (Distichoptilum gracile) and contained all genes standard to octocoral mitochondrial genomes (14 protein-coding genes, two ribosomal RNA genes and one transfer RNA). We found at least three different gene orders in Pennatulacea: the ancestral gene order, the gene order found in bamboo corals (Family Isididae), and a novel gene order. The mitogenome of one species of Umbellula has a bipartite genome (∼13 kbp and ∼5 kbp), with good evidence that both parts are circular.","PeriodicalId":54298,"journal":{"name":"Mitochondrial Dna Part a","volume":"18 1","pages":"764 - 777"},"PeriodicalIF":0.0,"publicationDate":"2019-07-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"81659860","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}
Pub Date : 2018-04-01DOI: 10.1080/24701394.2016.1278540
T. Giannoulis, C. Stamatis, Andreas Tsipourlianos, Z. Mamuris
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.
{"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}
Pub Date : 2018-04-01DOI: 10.1080/24701394.2016.1278537
Gen-Liang Li, Yi-Jiao Xu, Xiaomin Huang, Juan Xiao, Song Nong, Chao-gan Li
Abstract In this study, the methylation of mitochondrial genome in the immature testis of Chinese mitten crab Eriocheir sinensis of the Yangtze River system was determined for the first time using MeDIP-seq. Our methylated DNA fragments covered more than 99% of the mitochondrial genome in E. sinensis loaded from GenBank. There were 8 mutated bases and 42 SNPs in the crab mitochondrial genome. The methylation presented in all genes as well as in an A + T region, but less in intergenic regions in the mitochondrial genome. However, the level of methylation of most genes coding proteins and the A + T region were high. But, the majority of genes encoding tRNAs were hypomethylated, and both the rRNA genes also showed methylation of low or median frequency. Especially, the level of methylation of the intergenic regions is the lowest. Those features indicated that the methylation of DNA may play an important role in gene expressing regulation in the mitochondrial genome of immature testis in E. sinensis.
{"title":"MeDIP-seq reveals the features of mitochondrial genomic methylation in immature testis of Chinese mitten crab Eriocheir sinensis","authors":"Gen-Liang Li, Yi-Jiao Xu, Xiaomin Huang, Juan Xiao, Song Nong, Chao-gan Li","doi":"10.1080/24701394.2016.1278537","DOIUrl":"https://doi.org/10.1080/24701394.2016.1278537","url":null,"abstract":"Abstract In this study, the methylation of mitochondrial genome in the immature testis of Chinese mitten crab Eriocheir sinensis of the Yangtze River system was determined for the first time using MeDIP-seq. Our methylated DNA fragments covered more than 99% of the mitochondrial genome in E. sinensis loaded from GenBank. There were 8 mutated bases and 42 SNPs in the crab mitochondrial genome. The methylation presented in all genes as well as in an A + T region, but less in intergenic regions in the mitochondrial genome. However, the level of methylation of most genes coding proteins and the A + T region were high. But, the majority of genes encoding tRNAs were hypomethylated, and both the rRNA genes also showed methylation of low or median frequency. Especially, the level of methylation of the intergenic regions is the lowest. Those features indicated that the methylation of DNA may play an important role in gene expressing regulation in the mitochondrial genome of immature testis in E. sinensis.","PeriodicalId":54298,"journal":{"name":"Mitochondrial Dna Part a","volume":"138 1","pages":"335 - 339"},"PeriodicalIF":0.0,"publicationDate":"2018-04-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"86774463","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}
Pub Date : 2018-04-01DOI: 10.1080/24701394.2016.1278536
Z. Mirza, Harshil Patel
Abstract The monotypic colubrid snake genus Wallophis is revalidated and rediagnosed. Partial sequence for nuclear gene Oocyte maturation factor Mos (c-mos), mitochondrial Nicotinamide adenine dinucleotide dehydrogenase subunit 4 (ND4) and cytochrome b (cyt b) were used to assess phylogenetic relationship. Wallophis brachyura type species for the genus was found to be a member of the Western Palearctic clade of Colubrinae and is recovered as a sister taxa to Wallaceophis gujaratensis. Wallophis differs from Wallaceophis in an uncorrected pairwise p-distance of 17% for mitochondrial ND4 gene. Wallaceophis gujaratensis was described in three different spellings in the literature hence we here propose Wallaceophis gujaratensis as the correct spelling for the species based on provisions in the article 24.2.3. of the International Code for Zoological Nomenclature.
{"title":"Back from the dead! Resurrection and revalidation of the Indian endemic snake genus Wallophis Werner, 1929 (Squamata: Colubridae) insights from molecular data","authors":"Z. Mirza, Harshil Patel","doi":"10.1080/24701394.2016.1278536","DOIUrl":"https://doi.org/10.1080/24701394.2016.1278536","url":null,"abstract":"Abstract The monotypic colubrid snake genus Wallophis is revalidated and rediagnosed. Partial sequence for nuclear gene Oocyte maturation factor Mos (c-mos), mitochondrial Nicotinamide adenine dinucleotide dehydrogenase subunit 4 (ND4) and cytochrome b (cyt b) were used to assess phylogenetic relationship. Wallophis brachyura type species for the genus was found to be a member of the Western Palearctic clade of Colubrinae and is recovered as a sister taxa to Wallaceophis gujaratensis. Wallophis differs from Wallaceophis in an uncorrected pairwise p-distance of 17% for mitochondrial ND4 gene. Wallaceophis gujaratensis was described in three different spellings in the literature hence we here propose Wallaceophis gujaratensis as the correct spelling for the species based on provisions in the article 24.2.3. of the International Code for Zoological Nomenclature.","PeriodicalId":54298,"journal":{"name":"Mitochondrial Dna Part a","volume":"587 1","pages":"331 - 334"},"PeriodicalIF":0.0,"publicationDate":"2018-04-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"77059123","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}
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.
{"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}
Pub Date : 2018-02-17DOI: 10.1080/24701394.2016.1261851
Paramasivam Kameshpandian, Subhash Thomas, M. Nagarajan
Abstract Assessment of genetic diversity within and between populations is a prerequisite for sustainable utilization of domestic species. The domestic Muscovy duck (Cairina moschata) is an economically important species around the world for its unique meat taste and low-caloric content. It is one of the important domestic species in India as it ensures food security to the rural sectors. In this study, we have analyzed the genetic diversity and relationship of four Muscovy duck populations collected from different states (Assam, Mizoram, Odisha and Kerala) of India using mtDNA cytochrome b and nuclear DNA CYP2U1 genes. The results showed low genetic diversity among populations for both the genes. Kerala population showed significant genetic differences from the other three populations. The median joining network of cytochrome b gene suggested that the domestic Muscovy ducks present in India are the product of a single domestication event and probably introduced to India several years ago, as reported elsewhere. This study has also showed the suitability of nuclear DNA CYP2U1 gene in genetic diversity analysis.
{"title":"Genetic diversity and relationship of Indian Muscovy duck populations","authors":"Paramasivam Kameshpandian, Subhash Thomas, M. Nagarajan","doi":"10.1080/24701394.2016.1261851","DOIUrl":"https://doi.org/10.1080/24701394.2016.1261851","url":null,"abstract":"Abstract Assessment of genetic diversity within and between populations is a prerequisite for sustainable utilization of domestic species. The domestic Muscovy duck (Cairina moschata) is an economically important species around the world for its unique meat taste and low-caloric content. It is one of the important domestic species in India as it ensures food security to the rural sectors. In this study, we have analyzed the genetic diversity and relationship of four Muscovy duck populations collected from different states (Assam, Mizoram, Odisha and Kerala) of India using mtDNA cytochrome b and nuclear DNA CYP2U1 genes. The results showed low genetic diversity among populations for both the genes. Kerala population showed significant genetic differences from the other three populations. The median joining network of cytochrome b gene suggested that the domestic Muscovy ducks present in India are the product of a single domestication event and probably introduced to India several years ago, as reported elsewhere. This study has also showed the suitability of nuclear DNA CYP2U1 gene in genetic diversity analysis.","PeriodicalId":54298,"journal":{"name":"Mitochondrial Dna Part a","volume":"24 1","pages":"165 - 169"},"PeriodicalIF":0.0,"publicationDate":"2018-02-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"85027998","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}
Pub Date : 2018-02-17DOI: 10.1080/24701394.2016.1275596
S. Seddigh, M. Darabi
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.
{"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}
Pub Date : 2018-02-17DOI: 10.1080/24701394.2016.1275598
R. K. Negi, B. Joshi, J. Johnson, Rahul De, S. Goyal
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.
{"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}
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