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

DNA barcoding reveals cryptic species in the sea slater Ligia italica (Crustacea, Isopoda) from Tunisia. DNA 条形码揭示了突尼斯海蛞蝓 Ligia italica（甲壳纲，等足目）中的隐秘物种。

Mitochondrial DNA. Part A, DNA mapping, sequencing, and analysis Pub Date : 2024-06-20 DOI: 10.1080/24701394.2024.2363350

Nermine Laifi-Necibi, Nabil Amor, Paolo Merella, Osama Badri Mohammed, Lamia Medini

{"title":"DNA barcoding reveals cryptic species in the sea slater Ligia italica (Crustacea, Isopoda) from Tunisia.","authors":"Nermine Laifi-Necibi, Nabil Amor, Paolo Merella, Osama Badri Mohammed, Lamia Medini","doi":"10.1080/24701394.2024.2363350","DOIUrl":"https://doi.org/10.1080/24701394.2024.2363350","url":null,"abstract":"Barcoding studies have provided significant insights into phylogenetic relationships among species belonging to the genus Ligia (Crustacea, Isopoda). Herein the diversity of the Italian sea slater Ligia italica from Tunisia is studied for the first time. Samples were collected from 18 localities in Tunisia, and the analysis included previously published sequences from Italy and Greece available in GenBank. Bayesian and Maximum Likelihood phylogenetic analyses were carried out using a fragment of the mitochondrial COI gene. Putative cryptic species were explored using the 'barcode gap' approach in the software ASAP. A genetic landscape shape analysis was carried out using the program Alleles in Space. The analyses revealed highly divergent and well-supported clades of L. italica dispersed across Tunisia (Clades A1 and A2), Greece (Clade B) and Italy (Clades C1 and C2). High genetic dissimilarity among clades suggested that L. italica constitute a cryptic species complex. Divergence among different L. italica lineages (Clades A, B and C) occurred around 7-4.5 Ma. The detected high genetic distances among clades did not result from atypical mitochondrial DNAs or intracellular infection by Wolbachia bacteria. The complex history of the Mediterranean Sea appears to have played a significant role in shaping the phylogeographic pattern of Ligia italica. Additional morphological and molecular studies are needed to confirm the existence of cryptic species in Ligia italica in Mediterranean.","PeriodicalId":74204,"journal":{"name":"Mitochondrial DNA. Part A, DNA mapping, sequencing, and analysis","volume":" ","pages":"1-11"},"PeriodicalIF":0.0,"publicationDate":"2024-06-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141428491","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

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 DOI: 10.1080/24701394.2024.2345663

Nan Song, Shujun Wei, Miaomiao Wang

{"title":"Mitochondrial genome rearrangements and phylogenomics of the Hymenoptera (Insecta) using an expanded taxon sample.","authors":"Nan Song, Shujun Wei, Miaomiao Wang","doi":"10.1080/24701394.2024.2345663","DOIUrl":"https://doi.org/10.1080/24701394.2024.2345663","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":" 1241","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":"141127257","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

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

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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

Association between mitochondrial DNA genotype and sperm motility in humans. 人类线粒体 DNA 基因型与精子活力之间的关系。

Mitochondrial DNA. Part A, DNA mapping, sequencing, and analysis Pub Date : 2023-01-01 Epub Date: 2024-06-24 DOI: 10.1080/24701394.2024.2361609

Xueyou Song, Xiaoning Hong, Zilong Wang, Fuding Lu, Changze Song, Xinkun Wang, Xiaoyong Zhan, Jiaying Yu, Jiawen Zhai, Jiang Li, Xi Xiang, Xujun Xuan

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Correction.

Mitochondrial DNA. Part A, DNA mapping, sequencing, and analysis Pub Date : 2023-01-01 Epub Date: 2024-05-01 DOI: 10.1080/24701394.2024.2348847

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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 : 2023-01-01 Epub Date: 2024-04-07 DOI: 10.1080/24701394.2024.2332320

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":"10.1080/24701394.2024.2332320","DOIUrl":"10.1080/24701394.2024.2332320","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":"22-28"},"PeriodicalIF":0.0,"publicationDate":"2023-01-01","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

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 : 2023-01-01 Epub Date: 2024-05-16 DOI: 10.1080/24701394.2024.2345663

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":"10.1080/24701394.2024.2345663","DOIUrl":"10.1080/24701394.2024.2345663","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":"49-65"},"PeriodicalIF":0.0,"publicationDate":"2023-01-01","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

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