Mitochondrial DNA. Part A, DNA mapping, sequencing, and analysis最新文献_第2页

Mitochondrial genome rearrangements and phylogenomics of the Hymenoptera (Insecta) using an expanded taxon sample. 利用扩大的类群样本进行膜翅目（昆虫）线粒体基因组重排和系统发生组学研究。

Mitochondrial DNA. Part A, DNA mapping, sequencing, and analysis Pub Date : 2024-05-16

Nan Song, Shu-Jun Wei, Miaomiao Wang

{"title":"Mitochondrial genome rearrangements and phylogenomics of the Hymenoptera (Insecta) using an expanded taxon sample.","authors":"Nan Song, Shu-Jun Wei, Miaomiao Wang","doi":"","DOIUrl":"","url":null,"abstract":"The order Hymenoptera is one of the most species-rich insect orders, with more than 150,000 described extant species. Many hymenopteran insects have very different mitochondrial genome (mitogenome) organizations compared to the putative ancestral organization of insects. In this study, we sequenced 18 mitogenomes of representatives in the order Hymenoptera to increase taxonomic sampling. A total of 475 species were used in phylogenetic analyses, including 18 new mitogenomes and 457 existing mitogenomes. Using a site-heterogeneous model, Bayesian's inference from amino acid data yielded more resolved relationships among Hymenoptera than maximum-likelihood analysis and coalescent-based species analyses. The monophyly of Symphyta was not supported. The Xyeloidea was the earliest branching clade in the Hymenoptera. The Orussoidea was closely related to Apocrita. Within Apocrita, the Parasitoida was non-monophyletic. The monophyly of most Parasitoida superfamilies received strong support. The Proctotrupomorpha clade was supported in Bayesian's analysis. The Apoidea was monophyletic when excluding Ampulex compressa from consideration. The superfamilies Vespoidea and Chrysidoidea were found to be non-monophyletic. Comparisons of mitochondrial gene order revealed a higher frequency of gene rearrangement among lineages with a parasitoid lifestyle, particularly prominent in Chalcidoidea. The degree of gene rearrangement ranked second in specific taxa of Cynipoidea and Ichneumonoidea.","PeriodicalId":74204,"journal":{"name":"Mitochondrial DNA. Part A, DNA mapping, sequencing, and analysis","volume":" ","pages":"1-17"},"PeriodicalIF":0.0,"publicationDate":"2024-05-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140946645","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

Big jaw, small genome: first description of the mitochondrial genome of Odontomachus (Formicidae, Ponerinae): evolutionary implications for Ponerinae ants. 大颚，小基因组：首次描述Odontomachus（蚁科，蚁属）的线粒体基因组：对蚁属蚂蚁进化的影响。

Mitochondrial DNA. Part A, DNA mapping, sequencing, and analysis Pub Date : 2024-04-22

Maria Paula Villas-Bôas Tourinho Vidal, Igor Henrique Rodrigues-Oliveira, Iuri Batista Silva, Renan Rodrigues Rocha, Rubens Pasa, Karine Frehner Kavalco, Fabiano Bezerra Menegidio, Caroline Garcia

{"title":"Big jaw, small genome: first description of the mitochondrial genome of Odontomachus (Formicidae, Ponerinae): evolutionary implications for Ponerinae ants.","authors":"Maria Paula Villas-Bôas Tourinho Vidal, Igor Henrique Rodrigues-Oliveira, Iuri Batista Silva, Renan Rodrigues Rocha, Rubens Pasa, Karine Frehner Kavalco, Fabiano Bezerra Menegidio, Caroline Garcia","doi":"","DOIUrl":"","url":null,"abstract":"Mitochondrial DNA is a valuable tool for population genetics and evolutionary studies in a wide range of organisms. With advancements in sequencing techniques, it's now possible to gain deeper insights into this molecule. By understanding how many genes there are, how they're organized within the molecule, identifying the presence of spacers, and analyzing the composition of the D-Loop, we can better grasp the rearrangements that play a crucial role in the evolutionary dynamics of mitochondrial DNA. Additionally, phylogenetic analyses benefit significantly from having access to a larger pool of mtDNA genes. This wealth of genetic information allows for the establishment of evolutionary relationships with greater accuracy than ever before, providing a more robust framework than analyses based on a limited number of genes. Studies on mitogenomes belonging to the family Formicidae have proven promising, enabling the identification of gene rearrangements and enhancing our understanding of the internal relationships within the group. Despite this, the number of mitogenomes available for the subfamily Ponerinae is still limited, and here we present for the first time the complete mitogenome of Odontomachus. Our data reveal a gene duplication event in Formicidae, the first involving trnV, and new gene arrangements involving the trnM-trnI-trnQ and trnW-trnC-trnY clusters, suggesting a possible synapomorphy for the genus. Our phylogenetic analysis using the PCGs available for Formicidae supports the monophyly of the subfamily Ponerinae and sheds light on the relationship between Odontomachus and Pachycondyla.","PeriodicalId":74204,"journal":{"name":"Mitochondrial DNA. Part A, DNA mapping, sequencing, and analysis","volume":" ","pages":"1-12"},"PeriodicalIF":0.0,"publicationDate":"2024-04-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140869144","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

Mitogenomic analysis of Rüppell's fox (Vulpes rueppellii) confirms phylogenetic placement within the Palaearctic clade shared with its sister species, the red fox (Vulpes vulpes). 对吕佩尔狐（Vulpes rueppellii）的有丝分裂基因组分析证实了其在系统发育上与姊妹物种赤狐（Vulpes vulpes）同属古北欧支系。

Mitochondrial DNA. Part A, DNA mapping, sequencing, and analysis Pub Date : 2024-04-07

Ali Elsayed Basuony, Mostafa Saleh, Frank Hailer

{"title":"Mitogenomic analysis of Rüppell's fox (Vulpes rueppellii) confirms phylogenetic placement within the Palaearctic clade shared with its sister species, the red fox (Vulpes vulpes).","authors":"Ali Elsayed Basuony, Mostafa Saleh, Frank Hailer","doi":"","DOIUrl":"","url":null,"abstract":"The Rüppell's fox (Vulpes rueppellii) inhabits desert regions across North Africa, the Arabian Peninsula and southwestern Asia. Its phylogenetic relationship with other fox species, especially within the phylogeographic context of its sister species, V. vulpes, remain unclear. We here report the sequencing and de-novo assembly of the first annotated mitogenome of V. rueppellii, analysed with data from other foxes (tribe Vulpini, subfamily Caninae). We used four bioinformatic approaches to reconstruct the V. rueppellii mitogenome, obtaining identical sequences except for the incompletely assembled tandem-repeat region within the D-loop. The mitogenome displayed an identical organization, number and length of genes as V. vulpes. We found high support for clustering of both known subclades of V. rueppellii within the Palearctic clade of V. vulpes, rendering the latter species paraphyletic, consistent with previous analyses of shorter mtDNA fragments. More work is needed for a full understanding of the evolutionary drivers and consequences of hybridization in foxes.","PeriodicalId":74204,"journal":{"name":"Mitochondrial DNA. Part A, DNA mapping, sequencing, and analysis","volume":" ","pages":"1-7"},"PeriodicalIF":0.0,"publicationDate":"2024-04-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140871620","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

The complete mitochondrial genome and phylogenetic position of Schizothorax argentatus (Cyprinomorpha: Crypriniformes: Cyprinidae). Schizothorax argentatus（鲤形目：鲤形科：Cyprinidae）的完整线粒体基因组和系统发育位置。

Mitochondrial DNA. Part A, DNA mapping, sequencing, and analysis Pub Date : 2024-03-11

Zhengduan Huang, Dilina Rusitanmu, Jie Han

引用次数: 0

Opsarius siangi, a new Chedrinae fish species from the Brahmaputra drainage, India. Opsarius siangi，印度布拉马普特拉河流域的一种新的车鱼（Chedrinae）鱼种。

Mitochondrial DNA. Part A, DNA mapping, sequencing, and analysis Pub Date : 2024-02-02

Kavita Kumari, Simanku Borah, Sangeetha M Nair, Vettath Raghavan Suresh

{"title":"Opsarius siangi, a new Chedrinae fish species from the Brahmaputra drainage, India.","authors":"Kavita Kumari, Simanku Borah, Sangeetha M Nair, Vettath Raghavan Suresh","doi":"","DOIUrl":"","url":null,"abstract":"Opsarius siangi sp. nov., a previously undocumented species, has been identified from Siang River, Pasighat, Arunachal Pradesh, India. This newly described species is distinguished by a suite of unique morphological characteristics, notably including a complete lateral line, consisting of 65-77 scales, 32-39 pre-dorsal scales, 12-15 scales positioned between dorsal fin origin and lateral line, presence of two pairs of barbels, body depth ranging from 18.80% to 27.42% of standard length and a distinct pattern of 8-15 vertical bars adorning the body. A comprehensive genetic analysis was conducted by scrutinizing 78 Cytochrome oxidase I (COI) sequences extracted from Chedrinae fishes, with particular focus on Opsarius and Barilius genera. Phylogenetic analysis revealed that O. siangi sp. nov. occupies a distinctive clade, displaying close affinity with O. shacra. Intraspecific K2P genetic divergence, assessed at 0.02, falls well within established species delineation thresholds, while interspecific divergence in comparison to O. shacra was recorded at 0.112. Complementary species delimitation methodologies, including BIN and bPTP, further underscore taxonomic uniqueness of O. siangi sp. nov., within Chedrinae family. This description enriches our understanding of biodiversity within Siang River ecosystem and underscores the merit of employing multi-pronged approaches in taxonomic investigations.","PeriodicalId":74204,"journal":{"name":"Mitochondrial DNA. Part A, DNA mapping, sequencing, and analysis","volume":" ","pages":"1-12"},"PeriodicalIF":0.0,"publicationDate":"2024-02-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139673807","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

Correction. 校正

Mitochondrial DNA. Part A, DNA mapping, sequencing, and analysis Pub Date : 2022-01-01 Epub Date: 2022-07-21

引用次数: 0

DNA barcoding and delimitation of critically endangered indigenous and introduced tilapias (pisces cichlidae) of Pangani catchment, Northern Tanzania. 坦桑尼亚北部潘加尼集水区极度濒危的本土和引进罗非鱼（pisces cichlidae）的 DNA 条形码和划界。

Mitochondrial DNA. Part A, DNA mapping, sequencing, and analysis Pub Date : 2022-01-01 Epub Date: 2024-01-02

Yeremia Japhet Chuhila, Fred Demetrius Chibwana, Jestina Venance Katandukila, Chacha John Mwita

{"title":"DNA barcoding and delimitation of critically endangered indigenous and introduced tilapias (pisces cichlidae) of Pangani catchment, Northern Tanzania.","authors":"Yeremia Japhet Chuhila, Fred Demetrius Chibwana, Jestina Venance Katandukila, Chacha John Mwita","doi":"","DOIUrl":"","url":null,"abstract":"The Pangani catchment of Northern Tanzania harbours the critically endangered endemic tilapias of the genus Oreochromis. The introduction of non-native congenerics and consequent hybridization complicates taxa identification and phylogeny based on morphological systematics. We therefore morphologically and molecularly identified these tilapias and delimited their Molecular Operational Taxonomic Units (MOTUs) based on Cytochrome Oxidase Subunit I (CO1) gene for future management and conservation. A total of 132 indigenous and introduced tilapia specimens were morphologically identified, barcoded using the CO1 gene and delimited by Kimura 2 Parameter distance approaches, Automatic Barcode Gap Discovery (ABGD), Neighbour Joining (NJ) tree and haplotype analysis. Theoverall mean conspecific, congeneric and confamillial genetic distances based on the K2P model were 0.54%, 5.32% and 13.29% respectively. All taxa had a mean K2P distance < 2% and 90% (n = 10), were clearly delimited by the ABGD method. The NJ tree delimited tilapia taxa commensurate to the genetic distances depicted by DNA barcoding. However, DNA barcoding and NJ tree coherently failed to discriminate the morphologically distinct allopatric Oreochromis jipe and Oreochromis hunteri taxa. Moreover, the two methods depicted lack of monophyly in Oreochromis korogwe MOTUs implying that the taxon could consist of at least one MOTU. We conclude that the integration of morphological-based taxonomy and DNA barcoding among ichthyofaunal taxa herein will be invaluable in conservation and management of native tilapias in Pangani basin.","PeriodicalId":74204,"journal":{"name":"Mitochondrial DNA. Part A, DNA mapping, sequencing, and analysis","volume":" ","pages":"40-52"},"PeriodicalIF":0.0,"publicationDate":"2022-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139076141","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

Complete chloroplast genome of Lamiophlomis rotata: comparative genome analysis and phylogenetic analysis. Lamiophlomis rotata 的完整叶绿体基因组：比较基因组分析和系统发育分析。

Mitochondrial DNA. Part A, DNA mapping, sequencing, and analysis Pub Date : 2022-01-01 Epub Date: 2024-01-08

Ji Wang, Xing-Xing Mao, Yazhen Ma

{"title":"Complete chloroplast genome of Lamiophlomis rotata: comparative genome analysis and phylogenetic analysis.","authors":"Ji Wang, Xing-Xing Mao, Yazhen Ma","doi":"","DOIUrl":"","url":null,"abstract":"Lamiophlomis rotata, the only species within the genus Lamiophlomis (family Labiatae), exhibits a broad geographical distribution in elevated highland areas in Qinghai-Tibetan Plateau and possesses significant therapeutic properties. Numerous chemical compositions and putative phylogenetic affiliations of this species have been documented in prior research. Nevertheless, there is a scarcity of accessible publications regarding the genomic data of L. rotata, particularly its chloroplast genome. This dearth of knowledge hampers the comprehensive investigation of its phylogenetic placement within the Labiatae family. In this study, we present a comprehensive analysis of the plastid genome of L. rotata. The plastid genome has a length of 151,837 base pairs (bp) and a GC content of 38.5%. Within this genome, a total of 135 genes were identified, including 90 protein-coding genes, 37 transfer RNA (tRNA) genes, and eight ribosomal RNA (rRNA) genes. By employing phylogenetic analysis, the taxonomic position of L. rotata within the family Labiatae is elucidated, highlighting a close relationship between the genus Lamiophlomis and the genus Phlomis. Notably, extensive genetic variations were uncovered between L. rotata and other Phlomis species. This study could provide significant insights for understanding the phylogenetic relationships of taxa within Labiatae.","PeriodicalId":74204,"journal":{"name":"Mitochondrial DNA. Part A, DNA mapping, sequencing, and analysis","volume":" ","pages":"29-39"},"PeriodicalIF":0.0,"publicationDate":"2022-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139378959","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

Whole mitochondrial genome phylogeny of Drosophilidae. 果蝇科全线粒体基因组系统发育。

Mitochondrial DNA. Part A, DNA mapping, sequencing, and analysis Pub Date : 2022-01-01 Epub Date: 2024-01-25

Rob DeSalle, Sara Oppenheim, Patrick M O'Grady

{"title":"Whole mitochondrial genome phylogeny of Drosophilidae.","authors":"Rob DeSalle, Sara Oppenheim, Patrick M O'Grady","doi":"","DOIUrl":"","url":null,"abstract":"A total of 241 mitochondrial genomes were assembled and annotated from the SRA database to reconstruct a mtDNA genome phylogeny for the genus Drosophila, the family Drosophilidae, and close relatives. The resulting mtDNA genome phylogeny is largely congruent with previous higher-level analyses of Drosophila species with the exception of the relationships between the melanogaster, montium, anannassae, saltans and obscura groups. Although relationships within these species groups are congruent between nuclear and mtDNA studies, the mtDNA genome phylogeny of the groups is different when compared to earlier studies. Monophyly of known species groups within the genus Drosophila are highly supported and, as in previous work, the genera Lordiphosa, Hirtodrosophila, Zaprionus and Scaptomya are all imbedded within the genus Drosophila. Incongruence and partitioned support analyses indicate that DNA sequences are better at resolving the phylogeny than their translated protein sequences. Such analyses also indicate that genes on the minus strand of the circular molecule (Lrrna, Srrna, ND4, ND4L and ND5) provide most of the support for the overall phylogenetic hypothesis.","PeriodicalId":74204,"journal":{"name":"Mitochondrial DNA. Part A, DNA mapping, sequencing, and analysis","volume":" ","pages":"1-9"},"PeriodicalIF":0.0,"publicationDate":"2022-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139547593","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

Secondary contact of two cryptic Hokou gecko groups in the Izu Islands, Japan. 日本伊豆群岛两个隐居北口壁虎群的二次接触。

Mitochondrial DNA. Part A, DNA mapping, sequencing, and analysis Pub Date : 2022-01-01 Epub Date: 2024-01-29

Minoru Chiba, Daishi Yamazaki, Shun Ito, Osamu Kagawa, Satoshi Chiba

{"title":"Secondary contact of two cryptic Hokou gecko groups in the Izu Islands, Japan.","authors":"Minoru Chiba, Daishi Yamazaki, Shun Ito, Osamu Kagawa, Satoshi Chiba","doi":"","DOIUrl":"","url":null,"abstract":"We analyzed the mitochondrial DNA of Gekko hokouensis collected from the Izu Islands (maybe an introduced population) and the Nansei Islands (native population), both in Japan. A molecular phylogenetic analysis suggested that G. hokouensis of Japan belongs to a cryptic monophyletic group different from that of the currently discovered sample of China. Furthermore, the Japanese clade of G. hokouensis is differentiated into two subclades (Clade 1 and Clade 2 in this article). In the Nansei Islands, these two subclades form a complicated nested-distribution pattern and do not coexist on any of the islands, whereas both clades appear to coexist in the Izu Islands. The two clades exhibit high genetic diversity in the Nansei islands, which are the source population. Surprisingly, it has been revealed that high genetic diversity has also been maintained in the Izu Islands, which are the introduced population, in each clade. AMOVA has also revealed that the genetic differentiation between the populations in the Izu Islands and the Nansei Islands was not significant in each clade. These results suggest that the population of the Izu Islands is now in secondary contact between two clades by multiple migrations from various regions of the Nansei Islands.","PeriodicalId":74204,"journal":{"name":"Mitochondrial DNA. Part A, DNA mapping, sequencing, and analysis","volume":" ","pages":"53-60"},"PeriodicalIF":0.0,"publicationDate":"2022-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139577346","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