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

{"title":"High genetic diversity detected in the mitochondrial Control Region of the Serra Spanish Mackerel, <i>Scomberomorus brasiliensis</i> (Collette, Russo & Zavala, 1978) along the Brazilian coast.","authors":"Divino Bruno da Cunha, Kely Cristina Piedade Martins, José Nazareno do Santos Júnior, Edith Cibelle de Oliveira Moreira, Iracilda Sampaio, Cleonilde da Conceição Silva Queiroz, Maria Adriana Leite, Agerdânio Andrade de Souza, Carolina Aviz Dos Santos, Marcelo Vallinoto","doi":"","DOIUrl":"","url":null,"abstract":"<p><p>The Serra Spanish mackerel, <i>Scomberomorus brasiliensis</i>, is one of the most important fishery resources in the western tropical Atlantic, including northern and eastern Brazil. Despite its economic importance, few genetic markers have been sequenced in this species, and little is known of its population genetics. The present study evaluated the genetic variability of 110 individuals, representing three distinct Brazilian populations (Macapá, Fortaleza and Paranaguá), based on a segment of the mitochondrial Control Region. The sequences revealed high levels of genetic diversity, and suggested marked connectivity among the studied populations. A variable repeat was also found in the 3' portion of the studied Control Region fragment, which may prove useful as a marker in future genetic population studies of <i>S. brasiliensis</i>.</p>","PeriodicalId":74204,"journal":{"name":"Mitochondrial DNA. Part A, DNA mapping, sequencing, and analysis","volume":" ","pages":"178-185"},"PeriodicalIF":0.0,"publicationDate":"2021-07-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"10580391","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":"The mitochondrial genome of the endangered Spiny Butterfly Ray <i>Gymnura altavela</i> (Linnaeus 1758) (Myliobatiformes: Gymnuridae) provides insights into cryptic lineages.","authors":"Tabitha Cady, Katherine E Bemis, J Antonio Baeza","doi":"","DOIUrl":"","url":null,"abstract":"<p><p>The Spiny Butterfly Ray, <i>Gymnura altavela</i>, is found in tropical and temperate coastal waters with a discontinuous distribution: it occurs along the east coast of the United States of America, Brazil, and Uruguay in the western Atlantic Ocean, from Portugal to Angola in the eastern Atlantic, and also in the Mediterranean Sea. Globally, <i>Gymnura altavela</i> is considered endangered by the International Union for Conservation of Nature (IUCN). Our study analyzed the complete mitochondrial genome of <i>G. altavela</i> sequenced from an individual captured in the western Atlantic and compared it with a mitochondrial genome from a conspecific collected in the Mediterranean to explore if <i>G. altavela</i> comprises cryptic species. The newly assembled mitochondrial genome of <i>G. altavela</i> is 19,361bp in length and has 13 protein-coding genes (PCGs), two ribosomal RNA genes (<i>12s</i> ribosomal RNA and <i>16s</i> ribosomal RNA), 22 transfer RNA (tRNA) genes, and a 3,659 bp control region. The gene order is identical to that reported for the specimen collected in the Mediterranean and that of the congeneric Long-tailed Butterfly Ray, <i>G. poecilura</i>. A phylomitogenomic analysis based on translated PCGs supported the monophyly of the genus <i>Gymnura</i> and indicated that genetic dissimilarity between <i>G. altavela</i> from the western Atlantic Ocean and the Mediterranean Sea was greater than that calculated among congeneric species belonging to the genera <i>Mobula</i> and <i>Neotrygon</i>, similar to that calculated among congeneric stingrays in the genus <i>Hemitrygon</i>, but lower than that calculated among congeneric species in the genera <i>Pateobatis</i> and <i>Urogymnus</i>. Overall, our comparisons suggest that <i>G. altavela</i> comprises cryptic species or at least indicates considerable genetic structure between populations in the western Atlantic and Mediterranean. We present these findings in a phylomitogenomic analysis of other Myliobatiformes and Rhinopristiformes. Additional phylogeographic and taxonomic studies of <i>G. altavela</i> are needed to support conservation efforts for this endangered ray that may comprise cryptic evolutionary units.</p>","PeriodicalId":74204,"journal":{"name":"Mitochondrial DNA. Part A, DNA mapping, sequencing, and analysis","volume":" ","pages":"186-194"},"PeriodicalIF":0.0,"publicationDate":"2021-07-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"10153976","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":"Characterization and comparison of the mitochondrial genomes of the sea star <i>Asterias amurensis</i> (Echinodermata: Asteroidea) in East Asia.","authors":"Yanzhen Du, Kangkang Han, Xiaoqi Zeng, Gang Ni","doi":"","DOIUrl":"","url":null,"abstract":"<p><p>The starfish <i>Asterias amurensis</i> is a marine pest native to the northwestern Pacific and has successfully invaded southern Australia. <i>Asterias amurensis</i> have caused substantial environmental and economic impacts in both native and non-native regions. However, little information is available about the genetic features of its native populations, especially for those in North China. Here we sequenced the complete mitochondrial genomes of five individuals from different locations in China and compared their characteristics with three mitogenomes available from Japan. Multiple analyses and comparisons revealed little difference in the gene composition, gene order, codon usage, and nucleotide content among the eight mitogenomes. However, intraspecific phylogenetic reconstruction unveiled two divergent lineages between specimens from North China plus Ushimado (Seto Inland Sea, Japan) and northern Japan (Asamushi and Onagawa). This conclusion was backed by an analysis of pairwise genetic distances, which showed that individuals from different lineages had relatively higher values (all above 2%). Based on knowledge of paleoenvironmental and tectonic activity in the northwestern Pacific, the two lineages might have originated during the Early Pliocene due to the isolation of the East China Sea from the Japan Sea/East Sea during that time, while the present-day distribution of these lineages have likely been influenced by the ocean current system.</p>","PeriodicalId":74204,"journal":{"name":"Mitochondrial DNA. Part A, DNA mapping, sequencing, and analysis","volume":" ","pages":"212-219"},"PeriodicalIF":0.0,"publicationDate":"2021-07-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"71429941","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, population structure, and demographic history of the chilhuil sea catfish <i>Bagre panamensis</i> in Northwestern Mexico inferred from mitochondrial DNA.","authors":"Karla Isela Arroyo-Zúñiga, Jasmín Granados-Amores, Deivis Samuel Palacios-Salgado, Viridiana Peraza-Gómez, Fausto Valenzuela-Quiñonez","doi":"","DOIUrl":"","url":null,"abstract":"<p><p>The chilhuil sea catfish (<i>Bagre panamensis</i>) is an ecologically relevant species contributing to the structure, organization, and functioning of the ecosystems it inhabits. Also, it is an important artisanal fishery resource in the Mexican Pacific coast. This study aimed to determine the genetic diversity, population structure, and historical demography of <i>B. panamensis</i> in the Mexican Pacific. The mitochondrial DNA was amplified from two distinct regions, r16S and COI, resulting in an 1142 bp of the concatenated genes. Low genetic diversity levels were detected for r16S (<i>H</i> = 12; <i>h =</i> 0.131<i>; π</i> = <i>0.0003</i>) and high genetic diversity levels for COI (<i>H</i> = 57; <i>h =</i> 0.9128; <i>π = 0.0039</i>) and the concatenated gene fragments (<i>H</i> = 62; <i>h =</i> 0.9307; <i>π = 0.0023</i>). Population structure analysis indicated 'panmixia' for <i>B. panamensis</i> along the Mexican Pacific. Furthermore, historical demographic analysis (Tajima's <i>D</i>, Fu's <i>F</i>s, mismatch distribution, and Bayesian Skyline plot analyses) supported a population expansion scenario for the studied species.</p>","PeriodicalId":74204,"journal":{"name":"Mitochondrial DNA. Part A, DNA mapping, sequencing, and analysis","volume":" ","pages":"195-201"},"PeriodicalIF":0.0,"publicationDate":"2021-07-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"41241884","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":"Evaluating food web interactions among microcrustaceans and insect in a tropical shallow lake using DNA-based protocol.","authors":"Andrés R Domingos, Abner Carvalho-Batista, Rafael Robles, Marlene S Arcifa, Fernando L Mantelatto","doi":"","DOIUrl":"","url":null,"abstract":"<p><p>We developed species-specific primers of five microcrustacean preys, <i>Ceriodaphnia richardi</i>, <i>Diaphanosoma</i> cf<i>. brevireme</i>, <i>Daphnia gessneri, Simocephalus serrulatus, Thermocyclops decipiens</i> and <i>Mesocyclops</i> sp., to analyze food-web interactions involving their two insect predators <i>Rheumatobates crassifemur</i> and <i>Martarega uruguayensis</i> distributed in a tropical shallow lake. We designed internal primers of the COI gene (177-282 bp), and tested them, by means of PCR, for specificity and sensitivity. In our tests for specificity, all primers successfully amplified the DNA target but were species-specific failing to amplify the biomarker from any of the other species tested, even in a mixed DNA sample, including predators' DNA. In tests for sensitivity, primers successfully amplified zooplankton biomarkers from low concentration of DNA extractions and also from digestive tract of predators, even after many hours of ingestion. This technique provides a framework as an efficient tool for evaluation of food-web research in natural aquatic environments, where it is impossible to observe if predation occurs. Furthermore, this technique provides an effective solution for the identification of zooplankton species from the predator's digestive tract, where morphological identification alone is sometimes difficult because predators do not consume the prey but feeds using extra-oral digestion, such is the case of heteropterans.</p>","PeriodicalId":74204,"journal":{"name":"Mitochondrial DNA. Part A, DNA mapping, sequencing, and analysis","volume":" ","pages":"202-211"},"PeriodicalIF":0.0,"publicationDate":"2021-07-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"71429942","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":"Evolution, systematics, and the unnatural history of mitochondrial DNA.","authors":"Jeffrey H Schwartz","doi":"10.1080/24701394.2021.1899165","DOIUrl":"https://doi.org/10.1080/24701394.2021.1899165","url":null,"abstract":"<p><p>The tenets underlying the use of mtDNA in phylogenetic and systematic analyses are strict maternal inheritance, clonality, homoplasmy, and difference due to mutation: that is, there are species-specific mtDNA sequences and phylogenetic reconstruction is a matter of comparing these sequences and inferring closeness of relatedness from the degree of sequence similarity. Yet, how mtDNA behavior became so defined is mysterious. Even though early studies of fertilization demonstrated for most animals that not only the head, but the sperm's tail and mitochondria-bearing midpiece penetrate the egg, the opposite - only the head enters the egg - became fact, and mtDNA conceived as maternally transmitted. When midpiece/tail penetration was realized as true, the conceptions 'strict maternal inheritance', etc., and their application to evolutionary endeavors, did not change. Yet there is mounting evidence of paternal mtDNA transmission, paternal and maternal combination, intracellular recombination, and intra- and intercellular heteroplasmy. Clearly, these phenomena impact the systematic and phylogenetic analysis of mtDNA sequences.</p>","PeriodicalId":74204,"journal":{"name":"Mitochondrial DNA. Part A, DNA mapping, sequencing, and analysis","volume":"32 4","pages":"126-151"},"PeriodicalIF":0.0,"publicationDate":"2021-05-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1080/24701394.2021.1899165","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"25562951","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":"Character-based identification key for commercially important fishes of Pulicat lake: tool for conservation and management.","authors":"Rathipriya A,&nbsp;Kathirvelpandian A,&nbsp;Shanmugam S A,&nbsp;Suresh E,&nbsp;Felix N","doi":"10.1080/24701394.2021.1883009","DOIUrl":"https://doi.org/10.1080/24701394.2021.1883009","url":null,"abstract":"<p><p>Fishes are an important group of vertebrates in the animal world and make a significant contribution to global biodiversity. Fish is used as a source of food and contains many essential vitamins and fatty acids. The study of fish and their stability is important because, from year to year, fish stocks are often very important. For the conservation and management of these dwindling resources, correct identification of species is a prerequisite. Character-based methods of identification are of considerable use in this context, which classify specimens into species using classification rules that compactly describe species in terms of key diagnostic nucleotides in the gene sequences chosen. In this study, a total of 56 species of fishes distributed in Pulicat lake waters is taken as the target group. Mitochondrial CO1 sequences of each species were downloaded and modified. The species-specific diagnostic nucleotides for the selected group of species were identified using the BLOG version 2.0 software. Species-specific probes with a length range of 18-37 bp were designed on the basis of identified diagnostic nucleotide sites. The method is an effective tool for quickly and easily obtaining a significant amount of reliable information and could be used for forensic applications and conservation of fishes in Pulicat Lake.</p>","PeriodicalId":74204,"journal":{"name":"Mitochondrial DNA. Part A, DNA mapping, sequencing, and analysis","volume":"32 4","pages":"120-125"},"PeriodicalIF":0.0,"publicationDate":"2021-05-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1080/24701394.2021.1883009","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"25351547","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 population structure of the Blackspot seabream (<i>Pagellus bogaraveo</i>): contribution of mtDNA control region to fisheries management.","authors":"Joana I Robalo,&nbsp;Inês Farias,&nbsp;Sara M Francisco,&nbsp;Karen Avellaneda,&nbsp;Rita Castilho,&nbsp;Ivone Figueiredo","doi":"10.1080/24701394.2021.1882445","DOIUrl":"https://doi.org/10.1080/24701394.2021.1882445","url":null,"abstract":"<p><p>Marine fisheries management models have traditionally considered biological parameters and geopolitical boundaries. The result is the existence of fisheries management units that do not match genetic populations. However, this panorama is changing with the contribution of genetic and genomic data. <i>Pagellus bogaraveo</i> is a commercially important sparid in the northeast Atlantic, with three stock components being considered by ICES: the Celtic Sea and Bay of Biscay, Atlantic Iberian waters and the Azores. The northern stock collapsed (1975-1985) and is essential to characterize the genetic makeup of the species, particularly in the Iberian Peninsula, where it is managed as a single stock. The mitochondrial control region was used to screen the intraspecific diversity and population structure of individuals from six locations across the species range. The genetic diversity found is similar among sites, and there is differentiation between the Azores and the remaining locations.</p>","PeriodicalId":74204,"journal":{"name":"Mitochondrial DNA. Part A, DNA mapping, sequencing, and analysis","volume":"32 4","pages":"115-119"},"PeriodicalIF":0.0,"publicationDate":"2021-05-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1080/24701394.2021.1882445","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"25360619","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":"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":"10.1080/24701394.2021.1885389","url":null,"abstract":"<p><p>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 (<i>Eretmochelys imbricata</i>) and loggerhead turtles (<i>Caretta caretta</i>), 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 <i>ND4</i> and <i>ND5</i> in individual Cc2 with 16 and 38.6%, respectively. Of the tRNA genes, only tRNA^Tyr 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.</p>","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://www.ncbi.nlm.nih.gov/pmc/articles/PMC8179041/pdf/nihms-1706379.pdf","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}

{"title":"Cryptic species diversity and molecular diagnosis of <i>Channa orientalis</i>; an endemic freshwater fish of Sri Lanka.","authors":"Hansani Ekanayake,&nbsp;Naalin Perera,&nbsp;Kanishka D Ukuwela,&nbsp;Chaminda N Walpita,&nbsp;Suranga P Kodithuwakku,&nbsp;Sandun J Perera","doi":"10.1080/24701394.2021.1876040","DOIUrl":"https://doi.org/10.1080/24701394.2021.1876040","url":null,"abstract":"<p><p>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. <i>Channa orientalis</i> 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 <i>C. orientalis</i> and developed a DNA-based marker that permits accurate, low cost, and reliable identification of <i>C. orientalis</i>. Determination of genetic diversity was mainly carried out through genetic analysis of the mitochondrial <i>cytochrome c oxidase subunit 1</i> (<i>MT-CO1</i>) gene. The development of the DNA-based marker for the identification of <i>C. orientalis</i> 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 <i>C. orientalis</i> in Sri Lanka. The fast cost-effective gel-based PCR-RFLP marker method developed by us was successful in diagnosing <i>C. orientalis</i> 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.</p>","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}