Mitochondrial DNA. Part A, DNA mapping, sequencing, and analysis最新文献

{"title":"Molecular systematics and phylogeography of the genus <i>Alburnus</i> Rafinesque, 1820 (Teleostei, Leuciscidae) in Turkey.","authors":"Yusuf Bektas,&nbsp;Ismail Aksu,&nbsp;Cüneyt Kaya,&nbsp;Esra Bayçelebi,&nbsp;Fahrettin Küçük,&nbsp;Davut Turan","doi":"10.1080/24701394.2020.1791840","DOIUrl":"https://doi.org/10.1080/24701394.2020.1791840","url":null,"abstract":"<p><p>In this study, the phylogeny of <i>Alburnus</i> genus distributed in Turkish freshwaters was performed by analyzing mitochondrial cyt <i>b</i> gene (1141 bp) and COI gene (1551 bp) sequences from 1172 samples representing 112 populations of 24 species through their geographical distribution. According to our findings, 20 valid species are distributed in Turkey of which 18 have already been known. While six <i>Alburnus</i> species (<i>A. battalgilae, A. istanbulensis, A. carinatus, A. schischkovi, A. nasreddini ve A. adanensis</i>) have been synonomized, two new species (<i>Alburnus</i> sp.1 and <i>Alburnus</i> sp.2) from Dicle River and Çapraz Stream/Susurluk River have been identified. Extinct species such as <i>A</i>. <i>akili</i> and <i>A. nicaeensis</i> have not been observed <i>in situ</i>. Phylogenetic tree topologies and haplotype network of the 119 cyt <i>b</i> and 80 COI haplotypes detected in <i>Alburnus</i> species have indicated a consensus tree topology containing twenty lineages, each of corresponding to one species, and three <i>Alburnus</i> haplogroups corresponding to the geographical origins: Eastern Anatolia (I), Mediterranean (2) and Western & Northern Anatolia (3). The results indicate that the divergence between those haplogroups may have occurred during the Middle Miocene-Middle Pleistocene periods (from 14.9 to 5.29 million years).</p>","PeriodicalId":74204,"journal":{"name":"Mitochondrial DNA. Part A, DNA mapping, sequencing, and analysis","volume":"31 7","pages":"273-284"},"PeriodicalIF":0.0,"publicationDate":"2020-10-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1080/24701394.2020.1791840","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"38150180","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}

{"title":"DNA bar coding of Aplousobranchiata and Phlebobranchiata Ascidians (Phylum:Chordata) inferred from mitochondrial cytochrome oxidase subunit I (COI) gene sequence approach in Andaman and Nicobar Islands, India: a first report.","authors":"Rajaram Murugan,&nbsp;Gnanakkan Ananthan,&nbsp;Anandakumar Arunkumar","doi":"10.1080/24701394.2020.1798417","DOIUrl":"https://doi.org/10.1080/24701394.2020.1798417","url":null,"abstract":"<p><p>Ascidians (Phylum: Chordata) are sessile and filter-feeding marine animal, species identification of ascidians is possible by observing various morphological and anatomical features in various stages of life span. However, this method is labor intensive, time-consuming and very difficult for non-specialists particularly when dealing with field collections. Suborder Aplousobranchiata and Phlebobranchiata is the largest group of tunicates within, morphological and molecular data suggest that Didemnidae and Ascidiidae are monophyletic, but the monophyly of each genus and their phylogenetic relationships are still poorly understood. Therefore, this study was aimed to develop DNA barcodes of ascidians belonging to the orders of Aplousobranchiata and Phlebobranchiata species namely <i>Diplosoma listerianum</i>, <i>Lissoclinum fragile</i>, <i>Didemnum psammatode</i>, <i>Phallusia fumigata</i> and <i>Phallusia ingeria</i> collected from Andaman and Nicobar Islands were sequenced and submitted in Gen Bank. Colony structure, Scanning Electron Microscope (SEM) for spicules of colonial ascidians, larval type and zooids formation were found to be the most useful morphological characters for discriminating the species. Our BLAST results proved <i>D. Listerianum</i> KP842724 (98%) <i>L. fragile</i> KP842726 (100%) <i>D. psammatode</i> KP779902 (99%), <i>P. fumigata</i> KP779904 (99%) and <i>P. ingeria</i> KP842727 (100%) similarity and this is the first report of mitochondrial COI gene of these ascidians from Andaman and Nicobar Islands. We explored the usefulness of CO1 gene sequences for molecular level identification and mtDNA data in assessing a phylogenetic relationship of ascidian species.</p>","PeriodicalId":74204,"journal":{"name":"Mitochondrial DNA. Part A, DNA mapping, sequencing, and analysis","volume":"31 7","pages":"285-297"},"PeriodicalIF":0.0,"publicationDate":"2020-10-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1080/24701394.2020.1798417","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"38207921","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}

{"title":"Correction.","authors":"","doi":"10.1080/24701394.2020.1798057","DOIUrl":"https://doi.org/10.1080/24701394.2020.1798057","url":null,"abstract":"","PeriodicalId":74204,"journal":{"name":"Mitochondrial DNA. Part A, DNA mapping, sequencing, and analysis","volume":"31 7","pages":"311"},"PeriodicalIF":0.0,"publicationDate":"2020-10-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1080/24701394.2020.1798057","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"38183410","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}

{"title":"Phylogeography of the Japanese scad, <i>Decapterus maruadsi</i> (Teleostei; Carangidae) across the Central Indo-West Pacific: evidence of strong regional structure and cryptic diversity.","authors":"Noorul-Azliana Jamaludin,&nbsp;Wahidah Mohd-Arshaad,&nbsp;Noor Adelyna Mohd Akib,&nbsp;Danial-Hariz Zainal Abidin,&nbsp;Nguyen Viet Nghia,&nbsp;Siti-Azizah Mohd Nor","doi":"10.1080/24701394.2020.1799996","DOIUrl":"https://doi.org/10.1080/24701394.2020.1799996","url":null,"abstract":"<p><p>The Japanese scad <i>Decapterus maruadsi</i> (Carangidae) is an economically important marine species in Asia but its exploitation shows signs of overfishing. To document its stock structure, a population genetic and phylogeographic study of several populations of this species from the central part of the Indo-West Pacific region was conducted using the mitochondrial cytochrome <i>b</i> gene. Genetic homogeneity within the Sundaland region's population, including Rosario (the Philippines) and Ranong (Andaman Sea) populations was revealed with low nucleotide diversity (<i>π</i> = 0.001-0.003) but high haplotype diversity (<i>h</i> = 0.503-0.822). In contrast, a clear genetic structure was observed between this group and the northern Vietnam populations as revealed by <i>F</i>_ST, AMOVA and SAMOVA, while the central Vietnam population of Khanh Hoa is an admixed group between the two differentiated regional populations. The neutrality and mismatch distribution analyses supported a demographic expansion of <i>D. maruadsi</i> in between last Pleistocene to early Holocene period which influenced present day distribution pattern. Contemporary factors such as oceanic currents and different life history traits are also believed to play significant roles in the observed population structure and biogeographical pattern. Based on these results, recommendations on how stocks of the Japanese scad should be managed are offered.</p>","PeriodicalId":74204,"journal":{"name":"Mitochondrial DNA. Part A, DNA mapping, sequencing, and analysis","volume":"31 7","pages":"298-310"},"PeriodicalIF":0.0,"publicationDate":"2020-10-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1080/24701394.2020.1799996","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"38229309","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}

{"title":"Pediatric leukemia could be driven predominantly by non-synonymous variants in mitochondrial complex V in Mizo population from Northeast India.","authors":"Andrew Vanlallawma,&nbsp;Zothan Zami,&nbsp;Jeremy L Pautu,&nbsp;Zothankima Bawihtlung,&nbsp;Lalfakzuala Khenglawt,&nbsp;Doris Lallawmzuali,&nbsp;Lalchhandama Chhakchhuak,&nbsp;Nachimuthu Senthil Kumar","doi":"10.1080/24701394.2020.1786545","DOIUrl":"https://doi.org/10.1080/24701394.2020.1786545","url":null,"abstract":"<p><p>Leukemia is the most common childhood malignancy and studies had been carried out with promising revelations in its diagnosis and prognosis. However, majority of the studies are focused on nuclear alterations, while mitochondrial mutations are not well studied. Although there are studies of mitochondrial mutations in the adult leukemias, it does not represent the same for childhood malignancy. This is the first scientific report on the mtDNA mutational pattern of pediatric leukemic cases from a endogamous tribal population in Northeast India. <i>ATP6</i> involved in the Complex V was found to be more altered with respect to the Non-synonymous variants. mtDNA variations in the non-coding region (D-Loop - g.152 T>C) and in the coding region (MT-ND2, g.4824 A>G, p.T119A) showed a maternal inheritance which could reveal a genetic predisposition with lower penetrance. D-Loop variant (g.152 T>C) could be a diagnostic marker in accordance with previous report but is in contrast to pertaining only in AML - M3 subtype rather was found across in myeloid malignancies.</p>","PeriodicalId":74204,"journal":{"name":"Mitochondrial DNA. Part A, DNA mapping, sequencing, and analysis","volume":"31 6","pages":"245-249"},"PeriodicalIF":0.0,"publicationDate":"2020-08-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1080/24701394.2020.1786545","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"38107055","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}

{"title":"Evolutionary dissection of mtDNA hg H: a susceptibility factor for hypertrophic cardiomyopathy.","authors":"Christian M Hagen,&nbsp;Joanna L Elson,&nbsp;Paula L Hedley,&nbsp;Frederik H Aidt,&nbsp;Ole Havndrup,&nbsp;Morten K Jensen,&nbsp;Jørgen K Kanters,&nbsp;John J Atherton,&nbsp;Julie McGaughran,&nbsp;Henning Bundgaard,&nbsp;Michael Christiansen","doi":"10.1080/24701394.2020.1782897","DOIUrl":"https://doi.org/10.1080/24701394.2020.1782897","url":null,"abstract":"<p><p>Mitochondrial DNA (mtDNA) haplogroup (hg) H has been reported as a susceptibility factor for hypertrophic cardiomyopathy (HCM). This was established in genetic association studies, however, the SNP or SNP's that are associated with the increased risk have not been identified. Hg H is the most frequent European mtDNA hg with greater than 80 subhaplogroups (subhgs) each defined by specific SNPs. We tested the hypothesis that the distribution of H subhgs might differ between HCM patients and controls. The subhg H distribution in 55 HCM index cases was compared to that of two Danish mtDNA hg H control groups (<i>n</i> = 170 and <i>n</i> = 908, respectively). In the HCM group, H and 12 different H subhgs were found. All these, except subhgs H73, were also found in both control groups. The HCM group was also characterized by a higher proportion of H3 compared to H2. In the HCM group the H3/H2 proportion was 1.7, whereas it was 0.45 and 0.54 in the control groups. This tendency was replicated in an independent group of Hg H HCM index cases (<i>n</i> = 39) from Queensland, Australia, where the H3/H2 ratio was 1.5. In conclusion, the H subhgs distribution differs between HCM cases and controls, but the difference is subtle, and the understanding of the pathogenic significance is hampered by the lack of functional studies on the subhgs of H.</p>","PeriodicalId":74204,"journal":{"name":"Mitochondrial DNA. Part A, DNA mapping, sequencing, and analysis","volume":"31 6","pages":"238-244"},"PeriodicalIF":0.0,"publicationDate":"2020-08-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1080/24701394.2020.1782897","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"38105679","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}

{"title":"Comparative phylogenetic analysis of <i>Schizothorax plagiostomus</i> and <i>Schizothorax esocinus</i> with other members of subfamilies of cyprinidae on the basis of complete mitochondrial genome and 12S, 16S ribosomal RNA from Northren areas of Pakistan.","authors":"Aqsa Rehman,&nbsp;Muhammad Fiaz Khan,&nbsp;Saira Bibi,&nbsp;Mehreen Riaz,&nbsp;Faisal Nouroz","doi":"10.1080/24701394.2020.1787397","DOIUrl":"https://doi.org/10.1080/24701394.2020.1787397","url":null,"abstract":"<p><p>We assessed the relationship of Schizothoracinae species with other subfamilies Alburninae, Xenocyprinae, Cultrinae and Squaliobarbinae of family Cyprinidae by creating the phylogenetic trees using complete mitogenome and 12S and 16S RNA. Our representative species show the great affiliation with other but separated from a group composed of <i>Metzia mesembrinum</i>, <i>Metzia longinasus</i>, <i>Metzia lineata</i> and <i>Metzia formosae</i> of subfamily Alburninae while other subfamilies formed distinct group. The members of subfamily Schizothoracinae shows separate line of evolution from subfamily Barbinae.</p>","PeriodicalId":74204,"journal":{"name":"Mitochondrial DNA. Part A, DNA mapping, sequencing, and analysis","volume":"31 6","pages":"250-256"},"PeriodicalIF":0.0,"publicationDate":"2020-08-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1080/24701394.2020.1787397","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"38126257","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}

{"title":"Population genetic structure of the short-beaked common dolphin from the Black Sea and the Turkish Straits System.","authors":"Arda M Tonay,&nbsp;Begüm Uzun,&nbsp;Ayhan Dede,&nbsp;Ayaka Amaha Öztürk,&nbsp;Erdem Danyer,&nbsp;Işıl Aytemiz Danyer,&nbsp;Sabri Bilgin,&nbsp;Bayram Öztürk,&nbsp;Raşit Bilgin","doi":"10.1080/24701394.2020.1788008","DOIUrl":"https://doi.org/10.1080/24701394.2020.1788008","url":null,"abstract":"<p><p>Our study aims to assess the population connectivity, evolutionary history, and conservation status of the short-beaked common dolphin in the Black Sea and Turkish Straits System (TSS). We also include DNA sequences from the Atlantic Ocean and the Mediterranean Sea to provide a regional perspective to our localized study. Analysis of 366 base pairs of mitochondrial DNA D-loop fragments from 37 samples collected from short-beaked common dolphins in the Black Sea, TSS, and Aegean Sea revealed 13 haplotypes, eight of which have not been previously reported. While analysis of samples archived on GenBank revealed 89 different haplotypes across the region. The haplotype network contains two main peripheral groups that include individuals from all locations. Haplotypes from the Atlantic Ocean are scattered across the network and no obvious population separation was detected. Some shared haplotypes potentially indicate multi-directional colonization events of the Mediterranean Sea from the eastern Atlantic Ocean. Moreover, some less widely distributed haplotypes suggest some level of more recent genetic connectivity through the Strait of Gibraltar and the TSS and point out the importance of these straits in the dispersal of short-beaked common dolphins. The haplotype and nucleotide diversity values were lower in the Black Sea, TSS, and western Mediterranean Sea when compared to the Atlantic Ocean, supporting the expansion of Atlantic populations into the Mediterranean and the Black Seas. Differentiation was observed between the Atlantic Ocean, and the Mediterranean Sea, TSS and the Black Sea based on Фst but not between Mediterranean and the Black Seas. For common dolphins, which have high dispersal potential, the protection of open seas and narrow seaways to enhance connectivity may be crucial.</p>","PeriodicalId":74204,"journal":{"name":"Mitochondrial DNA. Part A, DNA mapping, sequencing, and analysis","volume":"31 6","pages":"257-264"},"PeriodicalIF":0.0,"publicationDate":"2020-08-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1080/24701394.2020.1788008","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"38143475","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}

{"title":"Genetic diversity and structure of the Chinese lake gudgeon (<i>Sarcocheilichthys sinensis</i>).","authors":"Xin-Hua Ding,&nbsp;Kui-Ching Hsu,&nbsp;Wen-Qiao Tang,&nbsp;Dong Liu,&nbsp;Yu-Min Ju,&nbsp;Hung-Du Lin,&nbsp;Jin-Quan Yang","doi":"10.1080/24701394.2020.1779239","DOIUrl":"https://doi.org/10.1080/24701394.2020.1779239","url":null,"abstract":"<p><p>Mitochondrial DNA cytochrome <i>b</i> and d-loop sequences (2,137 bp) in 65 specimens of <i>Sarcocheilichthys sinensis</i> from five populations were identified as two lineages (I and II). The pairwise genetic distance between lineages I and II was 1.94%. SAMOVA analyses suggested that the best grouping occurred at three groups, Yangtze, Qiantang and Minjiang Rivers. High haplotype diversity (0.949) and low nucleotide diversity (<i>θ</i>_π = 1.067%) were detected. The results of the neutrality tests, mismatch distribution and approximate Bayesian computation (ABC) did not support demographic expansions. The results of phylogenetic analysis, statistical dispersal-vicariance analysis (S-DIVA), ABC, MIGRATE-N and the time to the most recent common ancestor (T_MRCA) indicated two colonization routes. First, before the Wuyi Mountains lifted, <i>S. sinensis</i> dispersed from the Yangtze River to the Minjiang River. Second, during glaciation, the continental shelf was exposed, which contributed to the dispersion of populations from the Yangtze River.</p>","PeriodicalId":74204,"journal":{"name":"Mitochondrial DNA. Part A, DNA mapping, sequencing, and analysis","volume":"31 6","pages":"228-237"},"PeriodicalIF":0.0,"publicationDate":"2020-08-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1080/24701394.2020.1779239","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"38204460","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}

{"title":"Genetic identification of species and natural hybridization determination based on mitochondrial DNA and nuclear DNA of genus <i>Zacco</i> in Korea.","authors":"Philjae Kim,&nbsp;Jeong-Ho Han,&nbsp;Seung Lak An","doi":"10.1080/24701394.2020.1777994","DOIUrl":"https://doi.org/10.1080/24701394.2020.1777994","url":null,"abstract":"<p><p>Genus <i>Zacco</i> specimens collected in this study were classified genetically as five species, <i>Zacco platypus</i>, <i>Z. temminckii</i>, <i>Z. koreanus</i> and two unidentified species, using DNA barcoding analysis based on 655 bp of mitochondrial cytochrome <i>c</i> oxidase subunit I (<i>COI</i>) gene. Two of unidentified species (<i>Z</i>. sp.1 and <i>Z</i>. sp.2) were considered to be unrecorded or new species of genus <i>Zacco</i> according to genetic distances between <i>Zacco</i> species. In addition, we determined a natural hybrid based on polymorphic base at the diagnostic positions displayed on nuclear recombination activating gene 1 (<i>RAG1</i>) gene (965 bp), and estimated paternal and maternal species of natural hybrid comparing phylogenetic tree between <i>COI</i> and <i>RAG1</i>, and <i>Z</i>. sp.1♀ × <i>Z. koreanus</i>♂, <i>Z</i>. sp.2♀ × <i>Z. koreanus</i>♂ and <i>Z</i>. <i>koreanus</i>♀ × <i>Z.</i> sp.1♂ individuals were confirmed. The habitat of natural hybrids of <i>Z. koreanus</i> between <i>Z</i>. sp.1 and <i>Z</i>. sp.2 was identified as Geum and Yeongsan River, respectively. In our data, only F1 hybrid generation was identified; however, generations after F1 hybrid or backcross were not demonstrated.</p>","PeriodicalId":74204,"journal":{"name":"Mitochondrial DNA. Part A, DNA mapping, sequencing, and analysis","volume":"31 6","pages":"221-227"},"PeriodicalIF":0.0,"publicationDate":"2020-08-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1080/24701394.2020.1777994","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"38056185","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}