Mitochondrial DNA. Part A, DNA mapping, sequencing, and analysis最新文献_第5页

Detection of high heteroplasmy in complete loggerhead and hawksbill sea turtles mitochondrial genomes using RNAseq. 利用RNAseq检测红海龟和玳瑁海龟线粒体全基因组的高异质性。

Mitochondrial DNA. Part A, DNA mapping, sequencing, and analysis Pub Date : 2021-04-01 Epub Date: 2021-02-25 DOI: 10.1080/24701394.2021.1885389

David Delgado-Cano, Leonardo Mariño-Ramírez, Javier Hernández-Fernández

{"title":"Detection of high heteroplasmy in complete loggerhead and hawksbill sea turtles mitochondrial genomes using RNAseq.","authors":"David Delgado-Cano, Leonardo Mariño-Ramírez, Javier Hernández-Fernández","doi":"10.1080/24701394.2021.1885389","DOIUrl":"https://doi.org/10.1080/24701394.2021.1885389","url":null,"abstract":"Sea turtle populations around the world face rapid decline due to the effect of anthropogenic and environmental factors. Among the affected populations are those of hawksbill turtles (Eretmochelys imbricata) and loggerhead turtles (Caretta caretta), which is why a greater effort is currently being made in their monitoring and tracing. The intragenic degree of heteroplasmic mutations, commonly associated with diseases of variable symptoms, has not been analyzed in these species. In this study, heteroplasmy in the complete mitogenome (mtDNA) of three loggerhead turtles and one hawksbill turtle was identified from data obtained by RNAseq. Individuals Cc3, Ei1, Cc1 and Cc2 presented 0.3, 1.7, 1.8 and 7.1% of heteroplasmic mutations in all their mtDNA, respectively. The protein-coding genes that presented the highest percentage of heteroplasmy were ND4 and ND5 in individual Cc2 with 16 and 38.6%, respectively. Of the tRNA genes, only tRNATyr was heteroplasmic in the four individuals with 5.63% (Cc1), 25.35% (Ei1 and Cc2) and 49.3% (Cc3). In this study, we identified the critical sites of heteroplasmy in each individual and the genetic variability of their mitogenomes. The data obtained represents the baseline for future projects that evaluate the population status of these species.","PeriodicalId":74204,"journal":{"name":"Mitochondrial DNA. Part A, DNA mapping, sequencing, and analysis","volume":"32 3","pages":"106-114"},"PeriodicalIF":0.0,"publicationDate":"2021-04-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1080/24701394.2021.1885389","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"25404330","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Cryptic species diversity and molecular diagnosis of Channa orientalis; an endemic freshwater fish of Sri Lanka. 中国侧柏的隐种多样性及分子诊断斯里兰卡特有的淡水鱼。

Mitochondrial DNA. Part A, DNA mapping, sequencing, and analysis Pub Date : 2021-04-01 Epub Date: 2021-01-27 DOI: 10.1080/24701394.2021.1876040

Hansani Ekanayake, Naalin Perera, Kanishka D Ukuwela, Chaminda N Walpita, Suranga P Kodithuwakku, Sandun J Perera

{"title":"Cryptic species diversity and molecular diagnosis of Channa orientalis; an endemic freshwater fish of Sri Lanka.","authors":"Hansani Ekanayake, Naalin Perera, Kanishka D Ukuwela, Chaminda N Walpita, Suranga P Kodithuwakku, Sandun J Perera","doi":"10.1080/24701394.2021.1876040","DOIUrl":"https://doi.org/10.1080/24701394.2021.1876040","url":null,"abstract":"Fish genetic resources and diversity are very important aspects of environmental management and fisheries and are vital for making decisions on their commercial exploitation as well as conservation. The snakehead fishes in the world have significant economic importance as food and ornamental fish. A clear understanding of species' taxonomic status and genetic diversity is important for the utilization and implementation of conservation and management practices. Channa orientalis is a snakehead endemic to Sri Lanka that is heavily utilized in the ornamental fish export trade. Its genetic diversity has not yet been fully understood and it is difficult to distinguish it from closely resembling species. Therefore, we examined the genetic diversity of C. orientalis and developed a DNA-based marker that permits accurate, low cost, and reliable identification of C. orientalis. Determination of genetic diversity was mainly carried out through genetic analysis of the mitochondrial cytochrome c oxidase subunit 1 (MT-CO1) gene. The development of the DNA-based marker for the identification of C. orientalis was done through Polymerase Chain Reaction and Restriction Fragment Length Polymorphism (PCR-RFLP) analysis. Our analyses confirmed the presence of two distinct genetically divergent and geographically separated lineages of C. orientalis in Sri Lanka. The fast cost-effective gel-based PCR-RFLP marker method developed by us was successful in diagnosing C. orientalis from its closely resembling species. Thus, we believe our findings on the cryptic diversity and diagnostic methods will have important implications for the conservation and management of this endemic species.","PeriodicalId":74204,"journal":{"name":"Mitochondrial DNA. Part A, DNA mapping, sequencing, and analysis","volume":"32 3","pages":"77-84"},"PeriodicalIF":0.0,"publicationDate":"2021-04-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1080/24701394.2021.1876040","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"38865588","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 1

Higher-level phylogenetic relationships of rove beetles (Coleoptera, Staphylinidae) inferred from mitochondrial genome sequences. 从线粒体基因组序列推断花叶甲虫(鞘翅目，葡萄球菌科)的高级系统发育关系。

Mitochondrial DNA. Part A, DNA mapping, sequencing, and analysis Pub Date : 2021-04-01 Epub Date: 2021-02-11 DOI: 10.1080/24701394.2021.1882444

Nan Song, Qing Zhai, Yaling Zhang

{"title":"Higher-level phylogenetic relationships of rove beetles (Coleoptera, Staphylinidae) inferred from mitochondrial genome sequences.","authors":"Nan Song, Qing Zhai, Yaling Zhang","doi":"10.1080/24701394.2021.1882444","DOIUrl":"https://doi.org/10.1080/24701394.2021.1882444","url":null,"abstract":"Rove beetles (Staphylinidae) and allied families constitute a huge radiation of Coleoptera, but basal relationships in this group remain controversial. In this study, we newly sequenced eight mitogenomes of representatives of Staphylinidae by using next-generation sequencing method. Together with 99 existing mitogenomes of Staphyliniformia, (sub)family relationships were investigated with ML and Bayesian searches under various substitution models and data recoding schemes. The results consistently supported Scydmaenidae and Silphidae to be subordinate groups of Staphylinidae. Within the monophyletic Staphylinidae (including Scydmaenidae and Silphidae), the hypothesis of four major subfamily groups cannot be confirmed. Bayesian inferences under the site-heterogeneous mixture model generally supported the basal position of major clades corresponding to the Omaliine group. At the subfamily level, the monophyly of Pselaphinae, Oxytelinae, Scaphidiinae, Steninae and Staphylininae was supported. However, the subfamilies Omaliinae, Tachyporinae, Aleocharinae and Paederinae were each non-monophyletic.","PeriodicalId":74204,"journal":{"name":"Mitochondrial DNA. Part A, DNA mapping, sequencing, and analysis","volume":"32 3","pages":"98-105"},"PeriodicalIF":0.0,"publicationDate":"2021-04-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1080/24701394.2021.1882444","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"25356066","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 3

Phylogeography and demographic expansion in the widely distributed horned passalus beetle, Odontotaenius disjunctus (coleoptera: Passalidae). 分布广泛的有角passalus, Odontotaenius disjunctus的系统地理学和人口统计学扩展(鞘翅目:passalides科)。

Mitochondrial DNA. Part A, DNA mapping, sequencing, and analysis Pub Date : 2021-04-01 Epub Date: 2021-02-16 DOI: 10.1080/24701394.2021.1882443

Megan Whitaker, Taylor Procter, Frank M Fontanella

{"title":"Phylogeography and demographic expansion in the widely distributed horned passalus beetle, Odontotaenius disjunctus (coleoptera: Passalidae).","authors":"Megan Whitaker, Taylor Procter, Frank M Fontanella","doi":"10.1080/24701394.2021.1882443","DOIUrl":"https://doi.org/10.1080/24701394.2021.1882443","url":null,"abstract":"Dynamic climatic oscillations during the Pleistocene had profound effects on the distribution of species across North America. Although the role of historical climate change on speciation remains controversial, the impact on genetic variation within species has been well documented. Analyses of mtDNA sequences from the cytochrome oxidase I gene (911 bp) for 115 individuals of Odontotaenius disjunctus was combined with ecological niche modelling (ENM) to infer the demographic and population differentiation scenarios under present and past conditions. We inferred three lineages that diverged during the Pleistocene and replace each other geographically across the eastern United States. One of these lineages traverses previously identified genetic barriers for terrestrial animals including the Mississippi and Apalachicola Rivers and the Appalachian Mountains. We observed overlapping ranges between two haplotype groups as well as a region of secondary contact associated with ecological transition zone in northern Florida. The two continental lineages depict a genetic signature of a recent population increase associated with expanding niche envelope, whereas the clade restricted to peninsular Florida shows stable populations in a shrinking niche envelope. Given the lack of ecological separation, overlapping distribution of haplogroups and the presence of secondary contact zones, the taxonomic status of these lineages must await robust testing using multilocus DNA data to assess species boundaries.","PeriodicalId":74204,"journal":{"name":"Mitochondrial DNA. Part A, DNA mapping, sequencing, and analysis","volume":"32 3","pages":"85-97"},"PeriodicalIF":0.0,"publicationDate":"2021-04-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1080/24701394.2021.1882443","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"25373552","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 2

Mitochondrial ND1 T4216C and ND2 C5178A mutations are associated with maternally transmitted diabetes mellitus. 线粒体ND1 T4216C和ND2 C5178A突变与母体遗传的糖尿病有关。

Mitochondrial DNA. Part A, DNA mapping, sequencing, and analysis Pub Date : 2021-03-01 Epub Date: 2020-12-07 DOI: 10.1080/24701394.2020.1856101

Zhaochang Jiang, Lili Teng, Shunrong Zhang, Yu Ding

{"title":"Mitochondrial ND1 T4216C and ND2 C5178A mutations are associated with maternally transmitted diabetes mellitus.","authors":"Zhaochang Jiang, Lili Teng, Shunrong Zhang, Yu Ding","doi":"10.1080/24701394.2020.1856101","DOIUrl":"https://doi.org/10.1080/24701394.2020.1856101","url":null,"abstract":"Mutations in mitochondrial DNA (mtDNA) are important causes for type 2 diabetes mellitus (T2DM). To investigate the association between mtDNA mutations/variants and diabetes, we reported here clinical, genetic and biochemical characterization of a Chinese pedigree with maternally transmitted T2DM. Using PCR and direct sequencing analysis of mitochondrial genomes from the matrilineal relatives, we identified two potential pathogenic mutations, m.T4216C (p.Y304H) and m.C5178A (p.L237M) in the ND1 and ND2 genes, respectively, together with a set of genetic polymorphisms belonging to the human mitochondrial haplogroup D4b. Moreover, by isolating and analyzing polymononuclear leukocytes generated from the T2DM patients and controls, we identified lower levels of mitochondrial membrane potential and ATP production in T2DM patients than in the controls, in contrast, a significantly higher level of reactive oxygen species was observed in the T2DM patients carrying both of the m.T4216C and m.C5178A mutations (p < 0.05 for all). In addition, the plasma levels of malondialdehyde and 8-hydroxydeoxyguanosine in the T2DM patients markedly increased, while the level of superoxide dismutase decreased (p < 0.05 for all). Taken together, our data indicated that the ND1 T4216C and ND2 C5178A mutations may lead to oxidative stress and impair the mitochondrial function, and this, in turn, might have been involved in the pathogenesis and progression of T2DM in this pedigree. Thus, our study provides novel insight into the pathophysiology of T2DM that is manifested by mitochondrial dysfunction.","PeriodicalId":74204,"journal":{"name":"Mitochondrial DNA. Part A, DNA mapping, sequencing, and analysis","volume":"32 2","pages":"59-65"},"PeriodicalIF":0.0,"publicationDate":"2021-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1080/24701394.2020.1856101","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"38680148","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 15

Maternal inheritance of mitochondrial DNA in mice after inter-species hybridization and 138 generations of backcrossing. 种间杂交和回交138代后小鼠线粒体DNA的母系遗传。

Mitochondrial DNA. Part A, DNA mapping, sequencing, and analysis Pub Date : 2021-03-01 Epub Date: 2021-01-08 DOI: 10.1080/24701394.2020.1865940

Dan Wharton, Kevin C Morey, Robert Hanner

引用次数: 1

Expression of concern. 表达关心。

Mitochondrial DNA. Part A, DNA mapping, sequencing, and analysis Pub Date : 2021-03-01 Epub Date: 2021-01-11 DOI: 10.1080/24701394.2020.1857198

引用次数: 0

Morphological and molecular analysis of the freshwater copepod Heliodiaptomus viduus (Calanoida: Diaptomidae). 淡水桡足类双足鱼的形态与分子分析(鱼纲:双足鱼科)。

Mitochondrial DNA. Part A, DNA mapping, sequencing, and analysis Pub Date : 2021-03-01 Epub Date: 2020-11-12 DOI: 10.1080/24701394.2020.1845324

Mayavan Karthika, Shameem Shabana, Venkatachalam Ramasubramanian

{"title":"Morphological and molecular analysis of the freshwater copepod Heliodiaptomus viduus (Calanoida: Diaptomidae).","authors":"Mayavan Karthika, Shameem Shabana, Venkatachalam Ramasubramanian","doi":"10.1080/24701394.2020.1845324","DOIUrl":"https://doi.org/10.1080/24701394.2020.1845324","url":null,"abstract":"Morphological identification of the commonest Indian freshwater calanoid copepod Heliodiaptomus viduus has been facing a lot of controversies. To solve this problem, additional molecular support is needed. Hence, molecular analysis, along with morphological identification of the species using scanning electron microscopy (SEM) and optical microscopy, was carried out. The genetic distance between the intraspecific sequences in the 18SrRNA observed to be 0.000, while the interspecific distance within genus sequences varied from 0.000 to 0.002. Besides, it was noted that both the sequences (intraspecific) were present within a single clade of the phylogenetic trees with 100% bootstrap value. The genetic distance between the intraspecific sequences in the mtCOI observed to be 0.000, while the interspecific distance within genus sequences varied from 0.000 to 0.267 and lay in a separate clade in the phylogenetic tree from the within genus clade. Besides, it was noted that both the sequences (intraspecific) were present within a single clade of the phylogenetic tree with above 75% bootstrap value. Hence, the 18S rRNA (MH145356, MK457456) and mtCOI (MK621900) gene sequences of the present study are well supported the identification of H. viduus and it serves as the first molecular database besides providing morphological authentication (SEM images) of H.viduus. This combined analysis is envisioned to be helpful in selecting the ecologically and nutritionally important species for practical aquaculture.","PeriodicalId":74204,"journal":{"name":"Mitochondrial DNA. Part A, DNA mapping, sequencing, and analysis","volume":"32 2","pages":"43-58"},"PeriodicalIF":0.0,"publicationDate":"2021-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1080/24701394.2020.1845324","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"38594351","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Phylogeographic analyses of poplar revealed potential glacial refugia and allopatric divergence in southwest China. 杨树的系统地理学分析揭示了西南地区潜在的冰川避难所和异域分化。

Mitochondrial DNA. Part A, DNA mapping, sequencing, and analysis Pub Date : 2021-03-01 Epub Date: 2020-12-11 DOI: 10.1080/24701394.2020.1856828

Ang Li, Zhe Hou

{"title":"Phylogeographic analyses of poplar revealed potential glacial refugia and allopatric divergence in southwest China.","authors":"Ang Li, Zhe Hou","doi":"10.1080/24701394.2020.1856828","DOIUrl":"https://doi.org/10.1080/24701394.2020.1856828","url":null,"abstract":"The distribution pattern and genetic structure of plant species have been profoundly influenced by climate oscillations. Phylogeographic analyses have been numerously conducted in biodiversity hotspot regions and some general conclusions have been documented. However, other regions have received less attentions and these places may serve as potential glacial refugia for plant species to survive the Quaternary glaciation. Here, we used six nuclear and three cpDNA markers to estimate the phylogeographic pattern of Populus davidiana, a widespread species distributed in southwest China. As a widely distributed species in southwest China, the nucleotide diversity of P. davidiana was relatively high (Na = 6.28, HO = 0.534, and HE = 0.658). Genetic differentiation (FST) between the two main distribution regions, Yunnan and Guizhou provinces, was 0.21221. According to the composition of chloroplast haplotypes and the result of structure in these populations, we clearly distinguished two distantly sublineages corresponding to two distribution regions. Results of the Mantel test showed that there was a significant correlation between genetic distance and geographical distance (R2 = 0.8252, p<.05). The topographically heterogeneous regions and the low dispersal ability of seed and pollen may lead to high genetic differentiation between these two regions. A potential glacial refugia for P. davidiana located in adjacent regions to the Hengduan range was revealed and allopatric divergence in separated glacial refugia may directly lead to the present phylogeographic pattern of this species.","PeriodicalId":74204,"journal":{"name":"Mitochondrial DNA. Part A, DNA mapping, sequencing, and analysis","volume":"32 2","pages":"66-72"},"PeriodicalIF":0.0,"publicationDate":"2021-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1080/24701394.2020.1856828","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"38698890","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 1

Genetic diversity of Rhinogobius delicatus (Perciformes: Gobiidae): origins of the freshwater fish in East Taiwan. 台湾东部淡水鱼的遗传多样性(鳍形目:虾蛄科)

Mitochondrial DNA. Part A, DNA mapping, sequencing, and analysis Pub Date : 2021-01-01 Epub Date: 2020-11-10 DOI: 10.1080/24701394.2020.1844678

Yu-Min Ju, Jui-Hsien Wu, Kui-Ching Hsu, Yu-Wen Chiu, Wei-Kuang Wang, Chih-Wei Chen, Hung-Du Lin

{"title":"Genetic diversity of Rhinogobius delicatus (Perciformes: Gobiidae): origins of the freshwater fish in East Taiwan.","authors":"Yu-Min Ju, Jui-Hsien Wu, Kui-Ching Hsu, Yu-Wen Chiu, Wei-Kuang Wang, Chih-Wei Chen, Hung-Du Lin","doi":"10.1080/24701394.2020.1844678","DOIUrl":"https://doi.org/10.1080/24701394.2020.1844678","url":null,"abstract":"Mitochondrial DNA cytochrome b and d-loop sequences (1,984 bp) from 92 specimens of the freshwater goby Rhinogobius delicatus from seven drainages in East Taiwan were identified as two major lineages exhibiting a southern or northern distribution. The existence of low genetic diversity, a pattern of population decline and high population differentiation (FST=0.711) support the need for the development of management strategies for the conservation of localized populations. The results of a statistical dispersal-vicariance analysis suggested that the ancestral populations of R. delicatus were widely distributed in East Taiwan. Compared with the phylogeographic patterns of the other endemic eastern Taiwan freshwater fishes, Onychostoma alticorpus, Aphyocypris kikuckii and Hemimyzon taitungensis, our study suggests that the freshwater fishes colonized East Taiwan through northeastern and southwestern Taiwan, although the ancestral populations colonized the island before it reached its present shape.","PeriodicalId":74204,"journal":{"name":"Mitochondrial DNA. Part A, DNA mapping, sequencing, and analysis","volume":"32 1","pages":"12-19"},"PeriodicalIF":0.0,"publicationDate":"2021-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1080/24701394.2020.1844678","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"38592601","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 5