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

{"title":"Biological identification of ascidians from Vizhinjam Bay, southwest Coast of India using CO1 gene sequences.","authors":"Kaleemullah B Khan,&nbsp;L Praba,&nbsp;H Abdul Jaffar Ali","doi":"10.1080/24701394.2020.1772248","DOIUrl":"https://doi.org/10.1080/24701394.2020.1772248","url":null,"abstract":"<p><p>Ascidians are ecologically important components of marine ecosystems, yet the taxonomy and diversity of ascidians remain largely unexplored. Only <60% of reported ascidian species in India have been taxonomically described and identified and the rest of the species remain unidentified due to uncertainty in the morphology-based identification. We explored the usefulness of CO1 gene sequences for molecular level identification and mtDNA data in assessing phylogenetic relationships of 15 ascidian species. The mean sequence divergences within and among the species fell into the mean divergence ranges found in ascidian group. Species that are most similar grouped together formed a cluster. Clusters of species in a clade indicate that the species are closely related. Species that are highly divergent formed a separate branch. This study has concluded that the CO1 gene sequence is an effective tool to ascertain the molecular taxonomical studies on ascidians.</p>","PeriodicalId":74204,"journal":{"name":"Mitochondrial DNA. Part A, DNA mapping, sequencing, and analysis","volume":"31 5","pages":"209-217"},"PeriodicalIF":0.0,"publicationDate":"2020-07-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1080/24701394.2020.1772248","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"38024850","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":"Highlighting the classification of mitochondrial DNA haplogroups C and D in chickens.","authors":"Zhuoxian Weng,&nbsp;Xunhe Huang","doi":"10.1080/24701394.2020.1773452","DOIUrl":"https://doi.org/10.1080/24701394.2020.1773452","url":null,"abstract":"Mitochondrial DNA (mtDNA) has been widely used in tracing the matrilineal history of domestic chickens based on haplogroup trees generated by parsimony-like method (Lan et al. 2017). However, the increasing amount of data using different nomenclature for mtDNA phylogeny complicates comparisons across studies (Miao et al. 2013; Peng et al. 2015; LuzuriagaNeira et al. 2017; Huang et al. 2018; Al-Jumaili et al. 2020; Quan et al. 2020). A standardized, hierarchical haplogroup nomenclature system can benefit studies that involve matrilineal evolutionary genetics (Wang et al. 2014; Peng et al. 2015; Schr€ oder et al. 2016; Adeola et al. 2017; Wang et al. 2019; Zhang et al. 2020). Thus, a better understanding of chicken matrilineal genealogy urgently requires such a coherent nomenclature system. The common A–I nomenclature was first produced by Liu et al. (2006), using a phylogenetic framework to identify lineages based on a large D-loop dataset. However, because the D-loop has a high mutation rate and recurrent mutations, the structure of the matrilineal genealogy is often blurred. In response, a hierarchical haplogroup tree with the higher resolution was later constructed based on both D-loop sequences and mtDNA genomes (mtgenomes) (Miao et al. 2013). This updated tree retained the original nomenclature for haplogroups A–G, but defined several new haplogroups (H, I, and W–Z), sub-haplogroups (e.g. C1, C2, and C3), and macro-haplogroups (ABZY, CD, and EFGHIWX). Additionally, the nomenclature was altered if discordant between the D-loop and mtgenome. For instance, some sequences previously in clade C based on D-loop data became haplogroup X using mtgenome data, while other sequences originally in clade D were moved to haplogroups Y and C. Several clades of red junglefowl from Thailand were previously classified into haplogroup C based on D-loop information (Miao et al. 2013), were re-clustered as new haplogroup V at the basal branch of haplogroup CD (Huang et al. 2018). The classification of haplogroup C and D in chickens often changes depending on phylogeny construction methods, resulting in controversy. For example, recent definitions of these two groups (Quan et al. 2020) conflicted with those in the previous studies (Miao et al. 2013; Huang et al. 2018). Our reanalysis categorized only 33 sequences to sub-haplogroup C1, versus 236 sequences in Quan et al. (2020), and we also found that haplogroup C frequency in Southwest China was only 2.37% (Table S1). In another study, sub-haplogroup C2 in the nomenclature of Miao et al. (2013) was classified into haplogroup D (Table S2) (Al-Jumaili et al. 2020). This change may generate confusion for future studies because haplogroups C and D are increasingly used as potential candidate markers for exploring chicken origins and expansion, particularly in northern China and the Pacific (Miao et al. 2013; Xiang et al. 2014; Dyomin et al. 2017; Herrera et al. 2017; Zhang et al. 2017; Ulfah et al. 2017; Huang et al. ","PeriodicalId":74204,"journal":{"name":"Mitochondrial DNA. Part A, DNA mapping, sequencing, and analysis","volume":"31 5","pages":"218-219"},"PeriodicalIF":0.0,"publicationDate":"2020-07-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1080/24701394.2020.1773452","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"38025425","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":"Genetics of the Andean bear (<i>Tremarctos ornatus</i>; Ursidae, Carnivora) in Ecuador: when the Andean Cordilleras are not an Obstacle.","authors":"Manuel Ruiz-García,&nbsp;Armando Castellanos,&nbsp;Jessica Yanina Arias-Vásquez,&nbsp;Joseph Mark Shostell","doi":"10.1080/24701394.2020.1769088","DOIUrl":"https://doi.org/10.1080/24701394.2020.1769088","url":null,"abstract":"<p><p>One of the top carnivores in the Andean mountains is the Andean bear (<i>Tremarctos ornatus</i>, Ursidae), the only bear in South America. This is a flagship and key umbrella species in Ecuador because its conservation has a positive impact on the conservation of many other species in the Andes. But to preserve, first one must know the genetic characteristics of a species, among other things. For this, we analyzed six mitochondrial genes and seven nuclear DNA microsatellites of 108 Andean bear specimens sampled throughout Ecuador. We adopted three strategies for analyzing the data: by Province, by Region (north vs south), and by Cordillera. Four main results were obtained. First, the mitochondrial genetic diversity levels were elevated, but there were no differences in genetic diversity by Province or by Cordillera. By Regions, southern Ecuador had higher genetic diversity levels than to northern Ecuador. The genetic diversity for the microsatellites was only medium for the Andean bear at this country. Second, there was clear and significant evidence of female population expansions, for the overall sample, by Province, Region, and Cordillera. This population expansion was determined to have occurred in the time interval of 30,000-20,000 years ago (YA), during the last phase of the Pleistocene. We detected a population decrease to have occurred more recently, within the last 5000 years. It continued until about 300-200 YA when a population increase was again detected. Third, there were, practically, no phylogeographic pattern nor genetic differentiation among Andean bear populations in Ecuador by Province or by Cordillera for either mitochondrial or microsatellite markers. There was a little more genetic differentiation between northern and southern areas. Fourth, there was no trace of significant spatial genetic structure for the Andean bear in Ecuador in agreement with the genetic differentiation analyses. This shows that the Andean Cordilleras in this country did not present an obstacle to the dispersion of this species. Therefore, all of the Andean bear specimens in Ecuador should be treated as a unique Management Unit (MU) for conservation purposes, differently to that determined for other countries as Colombia.</p>","PeriodicalId":74204,"journal":{"name":"Mitochondrial DNA. Part A, DNA mapping, sequencing, and analysis","volume":"31 5","pages":"190-208"},"PeriodicalIF":0.0,"publicationDate":"2020-07-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1080/24701394.2020.1769088","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"37985364","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":"Characterizing coral reef biodiversity: genetic species delimitation in brachyuran crabs of Palmyra Atoll, Central Pacific.","authors":"Jennifer A Servis,&nbsp;Brendan N Reid,&nbsp;Molly A Timmers,&nbsp;Vasiliki Stergioula,&nbsp;Eugenia Naro-Maciel","doi":"10.1080/24701394.2020.1769087","DOIUrl":"https://doi.org/10.1080/24701394.2020.1769087","url":null,"abstract":"<p><p>Coral reefs are highly threatened ecosystems, yet there are numerous challenges in conducting inventories of their vanishing biodiversity, partly because many taxa remain difficult to detect and describe. Genetic species delimitation methods provide a standardized means for taxonomic classification including of cryptic, rare, or elusive groups, but results can vary by analytical method and genetic marker. In this study, a combination of morphological and genetic identification methods was used to estimate species richness and identify taxonomic units in true crabs (Infraorder Brachyura; n = 200) from coral reefs of Palmyra Atoll, Central Pacific. Genetic identification was based on matches between mitochondrial 16S ribosomal RNA (16S rRNA) and/or cytochrome <i>c</i> oxidase subunit I (COI) sequences to GenBank data, while morphological work relied on the taxonomic literature. Broad agreement in the number of candidate species delimited by genetic distance thresholds and tree-based approaches was found, although the multi-rate Poisson tree process (mPTP) was less appropriate for this dataset. The COI sequence data identified 30-32 provisional species and the 16S data revealed 34-35. The occurrence of 10 families, 20 genera, and 19 species of brachyurans at Palmyra was corroborated by at least two methods. Diversity levels within <i>Chlorodiella laevissima</i> indicated possible undescribed or cryptic species in currently lumped taxa. These results illustrate the efficacy of DNA sequences in identifying organisms and detecting cryptic variation, and underscore the importance of using appropriate genetic markers and multiple species delimitation analyses, with applications for future species descriptions.</p>","PeriodicalId":74204,"journal":{"name":"Mitochondrial DNA. Part A, DNA mapping, sequencing, and analysis","volume":"31 5","pages":"178-189"},"PeriodicalIF":0.0,"publicationDate":"2020-07-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1080/24701394.2020.1769087","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"38016186","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":"TaqMan real-time quantitative PCR for identification of antlers in tradition Chinese medicine.","authors":"Jie Pan,&nbsp;Rui Feng,&nbsp;Qing Hu,&nbsp;Hong Chen,&nbsp;Su Zhang,&nbsp;Jian Sun,&nbsp;Shen Ji","doi":"10.1080/24701394.2020.1741560","DOIUrl":"https://doi.org/10.1080/24701394.2020.1741560","url":null,"abstract":"<p><p>In this study, a method was established for discriminating the true <i>Cervus</i> antlers from its counterfeits using TaqMan real-time quantitative PCR. The method combines the use of true <i>Cervus</i> antlers-specific primers, that amplify a 226 bp fragment from true <i>Cervus</i> antlers DNA, and mammalian-specific primers amplifying a 146 bp fragment from mammalian species DNA, which are used as endogenous control. A TaqMan probe that hybridizes in the '<i>Cervus</i> antler' and also in the 'mammalian' DNA fragments is used to monitor the amplification of the target gene. The <i>Cervus</i> antler mitochondrial DNA was used as target gene to design the primers and TaqMan probes. The data revealed that the TaqMan real-time PCR-based assay can be used for identification of the true <i>Cervus</i> antlers from counterfeits in a single step. The limit of detection (LOD) was lower than 1 pg of DNA per reaction.</p>","PeriodicalId":74204,"journal":{"name":"Mitochondrial DNA. Part A, DNA mapping, sequencing, and analysis","volume":"31 5","pages":"173-177"},"PeriodicalIF":0.0,"publicationDate":"2020-07-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1080/24701394.2020.1741560","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"37909433","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":"Invalidation of taxa within the silvery wooly monkey (<i>Lagothrix lagothricha poeppigii</i>, Atelidae, Primates).","authors":"Manuel Ruiz-García,&nbsp;Myreya Pinedo-Castro,&nbsp;Aymara Albino,&nbsp;Jessica Yanina Arias-Vásquez,&nbsp;Armando Castellanos,&nbsp;Joseph Mark Shostell","doi":"10.1080/24701394.2020.1757084","DOIUrl":"https://doi.org/10.1080/24701394.2020.1757084","url":null,"abstract":"<p><p>The systematics of the Humboldt's wooly monkeys (<i>L. lagothricha</i>; Atelidae) is essential to preserve this Neotropical primate species. Traditionally, four morphological subspecies have been described, which recently have been molecularly confirmed. However, no population genetics studies have been carried out throughout the geographical distribution of one of these subspecies, <i>Lagothrix lagothricha poeppigii</i>. For this reason, we analyzed nine mitochondrial genes of <i>L. l. poeppigii</i> mainly collected from the Ecuadorian and Peruvian Amazon in order to better understand the evolutionary history of this taxon. The mitochondrial genetic diversity levels (haplotype and nucleotide diversity) we estimated are likely the highest yet reported for <i>L. lagothricha.</i> Our results did not detect important genetic structure within <i>L. l. poeppigii</i>. Furthermore, our phylogenetic analyses did not detect any relevant molecular cluster in the area where Groves hypothesized the existence of <i>L. poeppigii castelnaui</i>. Therefore, based on these data, <i>castelnaui</i> is not a valid taxon from a molecular perspective. The most differentiated subpopulation within <i>L. l. poeppigii</i> was from Morona-Santiago province (Ecuador) and had a genetic distance of 0.8-1.2% relative to the other subpopulations studied. However, this genetic distance range is within the variability found within a population. We estimated the mitochondrial temporal diversification within <i>L. l. poeppigii</i> to have occurred during the Pleistocene, 1.8-1.2 million years ago. Similarly, all our analyses detected a strong Pleistocene female population expansion for this taxon. Diverse spatial genetic analyses, perhaps with the exception of Monmonier's Algorithm, did not detect differentiated taxa within the area analyzed for <i>L. l. poeppigii</i>. These genetics results could be of importance to conservation efforts to preserve this taxon as one unit.</p>","PeriodicalId":74204,"journal":{"name":"Mitochondrial DNA. Part A, DNA mapping, sequencing, and analysis","volume":"31 4","pages":"147-162"},"PeriodicalIF":0.0,"publicationDate":"2020-05-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1080/24701394.2020.1757084","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"37868170","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":"Identification of Tibetan medicine Dida based on DNA barcoding.","authors":"Ruoshi Li,&nbsp;Shuixian Li,&nbsp;Xiaoquan Yang,&nbsp;Yongqiang Guo,&nbsp;Baozhong Duan,&nbsp;Li Xu,&nbsp;Conglong Xia","doi":"10.1080/24701394.2020.1741563","DOIUrl":"https://doi.org/10.1080/24701394.2020.1741563","url":null,"abstract":"<p><p>The purpose of this study was to test the ability of DNA barcoding to identify the herbal raw trade of Tibetan medicine Dida in China. A reference database for plant-material DNA barcodes was successfully constructed and used to identify 36 commercially samples of Dida collected from Southwest China. The ITS sequence was amplified from these samples and the efficiency of the PCR amplification of ITS was 100%. The DNA sequencing results revealed that 3 samples (8.3%) were authenticated as <i>Swertia chirayita</i>, 2 sequences (5.6%) were authenticated as <i>Swertia mussotii</i>, 3 sequences (8.3%) were authenticated as <i>Swertia ciliata</i>, as recorded in the Tibetan Pharmacopeia. The other samples were authenticated as adulterants and all of them originated from common plants belonging to <i>Saxifraga</i>, <i>Swertia</i> and <i>Halenia</i>. This result indicates Dida pieces that are available in the market have complex origins and may indicate a potential safety issue and DNA barcoding is a convenient tool for market supervision.</p>","PeriodicalId":74204,"journal":{"name":"Mitochondrial DNA. Part A, DNA mapping, sequencing, and analysis","volume":"31 4","pages":"131-138"},"PeriodicalIF":0.0,"publicationDate":"2020-05-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1080/24701394.2020.1741563","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"37789510","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":"Retraction: Complete mitochondrial genome of the Swan Goose (<i>Anser cygnoides</i> L.) and its phylogenetic analysis.","authors":"","doi":"10.1080/24701394.2020.1758395","DOIUrl":"https://doi.org/10.1080/24701394.2020.1758395","url":null,"abstract":"","PeriodicalId":74204,"journal":{"name":"Mitochondrial DNA. Part A, DNA mapping, sequencing, and analysis","volume":"31 4","pages":"172"},"PeriodicalIF":0.0,"publicationDate":"2020-05-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1080/24701394.2020.1758395","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"37869705","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":"Use of complete mitochondrial genome sequences to identify barcoding markers for groups with low genetic distance.","authors":"Aline Torres de Azevedo Chagas,&nbsp;Sandra Ludwig,&nbsp;Juliana da Silva Martins Pimentel,&nbsp;Nazaré Lúcio de Abreu,&nbsp;Daniela Lidia Nunez-Rodriguez,&nbsp;Hortensia Gomes Leal,&nbsp;Evanguedes Kalapothakis","doi":"10.1080/24701394.2020.1748609","DOIUrl":"https://doi.org/10.1080/24701394.2020.1748609","url":null,"abstract":"<p><p>Complete mitochondrial sequences can be rapidly obtained and are widely available, providing a great source of species information and allowing for the discovery of new specific molecular markers. However, for some taxonomic groups, traditional approaches for species delimitation are impaired by the low genetic distance values. In these cases, other species-level markers are used. For <i>Prochilodus</i>, which includes important neotropical fish species, species-level delimitation usually results in poor phylogenetic resolution when using mitochondrial COI/<i>cytB</i> genes as barcoding markers because of low genetic variability and low species-level resolution. Thus, in this study, we developed an approach to design and validate new barcoding markers with high species-level resolution obtained from the D-loop region, using <i>Prochilodus</i> spp. as a model. For the new barcoding marker validation, the amplicon region was used to infer the phylogenetic relationships of <i>Prochilodus</i> spp. through three distinct methods: Bayesian inference (BI), Neighbor-Joining method (NJ), and Maximum Likelihood method (ML). The phylogenetic relationships of <i>Prochilodus</i> spp. revealed high resolution at species-level, nonoverlapping clades, and high branch support. The genetic distance results allied to two different clustering methods (Bayesian Poisson tree processes and automatic barcode gap discovery) revealed the existence of a barcoding gap, thus, validating the use of the barcoding markers designed in this study. The approach proposed here may, therefore, be expanded to other taxa to access and validate new barcoding markers with higher resolution at the species level.</p>","PeriodicalId":74204,"journal":{"name":"Mitochondrial DNA. Part A, DNA mapping, sequencing, and analysis","volume":"31 4","pages":"139-146"},"PeriodicalIF":0.0,"publicationDate":"2020-05-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1080/24701394.2020.1748609","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"37854280","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":"Retraction: Complete mitochondrial genome of Paracobitis variegates and its phylogenetic analysis.","authors":"","doi":"10.1080/24701394.2020.1758393","DOIUrl":"https://doi.org/10.1080/24701394.2020.1758393","url":null,"abstract":"","PeriodicalId":74204,"journal":{"name":"Mitochondrial DNA. Part A, DNA mapping, sequencing, and analysis","volume":"31 4","pages":"171"},"PeriodicalIF":0.0,"publicationDate":"2020-05-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1080/24701394.2020.1758393","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"37869703","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}