Mitochondrial DNA. Part A, DNA mapping, sequencing, and analysis最新文献_第3页

Mitochondrial genome of the lesser known - Madras hedgehog (Paraechinus nudiventris): genomic characterization and comparative analysis within Erinaceidae. 鲜为人知的马德拉斯刺猬（Paraechinus nudiventris）的线粒体基因组：基因组特征和狐尾科的比较分析。

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Mitochondrial DNA. Part A, DNA mapping, sequencing, and analysis Pub Date : 2026-01-01 Epub Date: 2026-04-04 DOI: 10.1080/24701394.2026.2648118

Thapasya Vijayan, Harald Meimberg, Brawin Kumar

{"title":"Mitochondrial genome of the lesser known - Madras hedgehog (Paraechinus nudiventris): genomic characterization and comparative analysis within Erinaceidae.","authors":"Thapasya Vijayan, Harald Meimberg, Brawin Kumar","doi":"10.1080/24701394.2026.2648118","DOIUrl":"10.1080/24701394.2026.2648118","url":null,"abstract":"The Madras hedgehog (Paraechinus nudiventris) is an understudied species endemic to southern India, with limited genetic data available for understanding its evolutionary history. Here, we present the complete mitochondrial genome (17,232 bp), annotated and analysed in comparison with other Erinaceidae species. The mitogenome retains the typical vertebrate structure, comprising 13 protein-coding genes, 22 tRNAs, two rRNAs, and a non-coding control region, with an A + T rich nucleotide composition. Phylogenetic analyses using Bayesian and maximum-likelihood approaches confirmed the species' placement within Paraechinus, with divergence from P. micropus estimated during the Pleistocene. Molecular evolutionary analyses revealed selective constraints on oxidative phosphorylation genes, with atp8 showing the highest variability. Our divergence time estimates, incorporating fossil calibrations, refine the evolutionary timeline of Erinaceidae, providing insights into the diversification of hedgehogs in South Asia. By making this annotated mitochondrial genome publicly available, we provide a foundational resource for future studies on the genetic diversity, phylogeography, and conservation of P. nudiventris and its relatives.","PeriodicalId":74204,"journal":{"name":"Mitochondrial DNA. Part A, DNA mapping, sequencing, and analysis","volume":" ","pages":"1-10"},"PeriodicalIF":0.6,"publicationDate":"2026-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147619141","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

Characterization of the complete mitochondrial genome of the beetle Chrysolina exanthematica (Chrysomelidae: Chrysomelinae) and phylogenetic implications. 金菊科金菊甲虫（Chrysolina exanthematica）线粒体全基因组特征及其系统发育意义。

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Mitochondrial DNA. Part A, DNA mapping, sequencing, and analysis Pub Date : 2026-01-01 Epub Date: 2026-04-18 DOI: 10.1080/24701394.2026.2658511

Laizheng Jiao, Yu Chen

{"title":"Characterization of the complete mitochondrial genome of the beetle Chrysolina exanthematica (Chrysomelidae: Chrysomelinae) and phylogenetic implications.","authors":"Laizheng Jiao, Yu Chen","doi":"10.1080/24701394.2026.2658511","DOIUrl":"10.1080/24701394.2026.2658511","url":null,"abstract":"The rapid development of next-generation sequencing (NGS) has greatly accelerated research on insect mitochondrial genomes (mitogenomes), which are now widely used in phylogenetics, population genetics, and species identification. Here, we sequenced and characterized the complete mitogenome of Chrysolina exanthematica, an economically important pest of medicinal plants in the subfamily Chrysomelinae. The mitogenome was 16,177 bp in length with an AT content of 78.46%, comprising the canonical 37 genes found in insect mitogenomes, including 13 protein-coding genes (PCGs), 22 transfer RNA genes (tRNAs), and two ribosomal RNA genes (rRNAs), as well as a putative control region (CR) of 1,553 bp. The Ka/Ks ratios of all 13 PCGs within Chrysolina were below 1, indicating that they were subject to purifying selection. Extensive taxon sampling revealed that Oreina alpestris was nested within the Chrysolina clade, forming a strongly supported sister-group relationship with C. exanthematica (BS = 97%, PP = 1.00) in both maximum likelihood and Bayesian inference analyses, thus demonstrating the non-monophyly of Chrysolina. Furthermore, the mitogenome characterized here provides reliable molecular markers for the accurate identification of this economically important leaf beetle.","PeriodicalId":74204,"journal":{"name":"Mitochondrial DNA. Part A, DNA mapping, sequencing, and analysis","volume":" ","pages":"21-32"},"PeriodicalIF":0.6,"publicationDate":"2026-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147719059","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

Characterisation and comparative analysis of the complete mitochondrial genomes of two whiprays, Himantura leoparda and H. uarnak, occurring in the Southwest Indian Ocean. 西南印度洋两种鞭鳐（Himantura leoparda和H. warnak）线粒体全基因组的特征和比较分析。

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Mitochondrial DNA. Part A, DNA mapping, sequencing, and analysis Pub Date : 2025-10-01 Epub Date: 2026-02-02 DOI: 10.1080/24701394.2026.2622715

Karla Redelinghuys, Juliana D Klein, Rhett H Bennett, Stephanie Venables, Andrea Marshall, Aletta E Bester-van der Merwe

{"title":"Characterisation and comparative analysis of the complete mitochondrial genomes of two whiprays, Himantura leoparda and H. uarnak, occurring in the Southwest Indian Ocean.","authors":"Karla Redelinghuys, Juliana D Klein, Rhett H Bennett, Stephanie Venables, Andrea Marshall, Aletta E Bester-van der Merwe","doi":"10.1080/24701394.2026.2622715","DOIUrl":"10.1080/24701394.2026.2622715","url":null,"abstract":"The genus Himantura, Müller and Henle 1837 (Myliobatiformes: Dasyatidae) comprises benthic stingrays inhabiting tropical and subtropical waters, including the biodiversity-rich Southwest Indian Ocean (SWIO). Despite their ecological significance and susceptibility to anthropogenic pressures, the genetic diversity and evolutionary relationships of Himantura species remain poorly understood. This study sequenced and characterised the complete mitochondrial genomes of the SWIO variants of Himantura leoparda (17,682 bp) and Himantura uarnak (17,670 bp), the latter representing the first mitogenome for this species. Each mitogenome exhibited the typical vertebrate structure: 13 protein-coding genes (PCGs), 22 transfer RNA genes, two ribosomal RNA genes, and a control region. Codon usage was strongly AT-biased, with leucine (CTA) and isoleucine (ATC) predominating. Elevated single nucleotide polymorphism diversity in ND4 suggests ongoing divergence with adaptive implications. Phylogenetic analysis of concatenated PCGs confirmed the monophyly of Himantura within Dasyatidae, with distinct separation between the two SWIO mitogenomes supporting recognition of two separate species. The SWIO H. leoparda variant was most closely related to the Indo-Pacific H. leoparda variant. These findings address taxonomic ambiguities within the genus and highlight the need for species-specific conservation strategies, providing essential mitogenomic data to support future Himantura research in the SWIO.","PeriodicalId":74204,"journal":{"name":"Mitochondrial DNA. Part A, DNA mapping, sequencing, and analysis","volume":" ","pages":"237-248"},"PeriodicalIF":0.6,"publicationDate":"2025-10-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"146108844","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

DNA barcoding for identification of ichthyofauna in Pantabangan Dam, Nueva Ecija, Philippines. 菲律宾新埃西加省潘塔班甘大坝鱼类的DNA条形码鉴定。

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Mitochondrial DNA. Part A, DNA mapping, sequencing, and analysis Pub Date : 2025-10-01 Epub Date: 2026-02-19 DOI: 10.1080/24701394.2026.2631395

Simon G Alcantara, Claire Samantha T Juanico, Alexander Ordynets, Marjeline C Fernandez, Apolinario V Yambot

{"title":"DNA barcoding for identification of ichthyofauna in Pantabangan Dam, Nueva Ecija, Philippines.","authors":"Simon G Alcantara, Claire Samantha T Juanico, Alexander Ordynets, Marjeline C Fernandez, Apolinario V Yambot","doi":"10.1080/24701394.2026.2631395","DOIUrl":"10.1080/24701394.2026.2631395","url":null,"abstract":"The present study established the first molecular-based inventory of nine freshwater fish species from Pantabangan Dam, a genetically unexplored fishery resource in Nueva Ecija, Central Luzon region of the Philippines. Forty mitochondrial cytochrome c oxidase I (COI) sequences were generated representing nine species, eight families and six orders of fishes, providing potential application in biodiversity assesment and management. In all cases, sequence analysis yielded low intraspecific divergence and a high interspecific genetic distance was observed in the Nearest Neighbor Distance analysis. Neighbor-Joining and Maximum Likelihood phylogenetic trees recovered a monophyletic species-level clades supported by high bootstrap values. Out of the nine species identified, three were native species in the Philippines (Leiopotherapon plumbeus, Glossogobius aureus and Clarias batrachus). Two species (Micropterus floridanus and Coptodon zillii) have been recorded for the first time in the dam, indicating the need to review how monitoring protocols can be enhanced by combining morphological assessment and molecular identification. The generated sequences can be used as a baseline data for the conservation of endemic species and formulation of management decisions on the invasive fishes. Overall, our study confirmed the efficiency of DNA barcoding in species delineation and offered a new framework for fish management in the dam.","PeriodicalId":74204,"journal":{"name":"Mitochondrial DNA. Part A, DNA mapping, sequencing, and analysis","volume":" ","pages":"249-256"},"PeriodicalIF":0.6,"publicationDate":"2025-10-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"146230200","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

Nemerteans Emplectonema ex gr. gracile (Johnston 1837) (Hoplonemertea, Monostilifera) from the Sea of Okhotsk, Sea of Japan, and Yellow Sea. 来自鄂霍次克海、日本海和黄海的Nemerteans Emplectonema ex grg . gracile (Johnston 1837) （Hoplonemertea, Monostilifera）。

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Mitochondrial DNA. Part A, DNA mapping, sequencing, and analysis Pub Date : 2025-10-01 Epub Date: 2025-12-15 DOI: 10.1080/24701394.2025.2602435

Anna A Martynova, Jin Wu, Shi-Chun Sun, Alexei V Chernyshev

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The mitochondrial genome of Palythoa tuberculosa (Esper, 1805) contains a novel ORF with unknown function. Palythoa tuberlosa （Esper, 1805）线粒体基因组包含一个功能未知的新ORF。

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Mitochondrial DNA. Part A, DNA mapping, sequencing, and analysis Pub Date : 2025-10-01 Epub Date: 2026-03-27 DOI: 10.1080/24701394.2026.2647326

Yuki Yoshioka, Megumi Kanai, Tomofumi Nagata, Noriyuki Satoh

{"title":"The mitochondrial genome of Palythoa tuberculosa (Esper, 1805) contains a novel ORF with unknown function.","authors":"Yuki Yoshioka, Megumi Kanai, Tomofumi Nagata, Noriyuki Satoh","doi":"10.1080/24701394.2026.2647326","DOIUrl":"10.1080/24701394.2026.2647326","url":null,"abstract":"Recent advances in sequencing technology have enabled rapid and cost-effective recovery of mitochondrial genomes (mitogenomes), which are used in phylogenetic and evolutionary studies. Among cnidarians, the order Zoantharia possesses one of the largest mitogenomes on average 20,976 bp. Palythoa tuberculosa (Hexacorallia: Zoantharia: Sphenopidae) has the largest reported mitogenome in this order (23,044 bp), approximately 2,000 bp larger than the zoantharian average. In this study, to determine the basis of this expansion, we generated and annotated the complete mitogenome of P. tuberculosa. Synteny analysis revealed that this increased genome size is attributed to the insertion of a novel open reading frame (ORF) located between trnW and cox2, encoding 665 amino acids, initiated with the codon ATG and terminated with TAA. This ORF was also present in the closely related species P. caribaeorum, suggesting its origin in their common ancestor. This represents the first case of a novel ORF insertion in zoantharians and demonstrates that mitogenome expansion in zoantharians can result from lineage-specific protein-coding insertions, revealing greater structural dynamism in anthozoan mitogenomes than previously recognized.","PeriodicalId":74204,"journal":{"name":"Mitochondrial DNA. Part A, DNA mapping, sequencing, and analysis","volume":" ","pages":"257-262"},"PeriodicalIF":0.6,"publicationDate":"2025-10-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147535041","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

Characterization of genetic diversity of unicorn leatherjacket filefish, Aluterus monoceros (Linnaeus, 1758) along the Indian Coast using mitochondrial DNA markers. 利用线粒体DNA标记对印度海岸独角兽皮麻鱼al子宫monoceros （Linnaeus, 1758）遗传多样性的分析。

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Mitochondrial DNA. Part A, DNA mapping, sequencing, and analysis Pub Date : 2025-10-01 Epub Date: 2025-10-21 DOI: 10.1080/24701394.2025.2577475

Kamei Lanthaimeilu, Asha Taterao Landge, Binaya Bhusan Nayak, Shashi Bushan, Jeevan Thiruguna Mallegowda, Dayal Devadas, Murugesan SriHari, Annam Pavan-Kumar

{"title":"Characterization of genetic diversity of unicorn leatherjacket filefish, Aluterus monoceros (Linnaeus, 1758) along the Indian Coast using mitochondrial DNA markers.","authors":"Kamei Lanthaimeilu, Asha Taterao Landge, Binaya Bhusan Nayak, Shashi Bushan, Jeevan Thiruguna Mallegowda, Dayal Devadas, Murugesan SriHari, Annam Pavan-Kumar","doi":"10.1080/24701394.2025.2577475","DOIUrl":"10.1080/24701394.2025.2577475","url":null,"abstract":"Aluterus monoceros, commonly known as the Unicorn leatherjacket filefish, has a circumglobal distribution and was infrequently recorded in Indian trawl landings prior to 2008. In recent years, substantial catches have been reported from major fish landing centres along the Indian coast, establishing it as a targeted fishery. Despite its growing commercial importance, the population structure of this species remains largely unexplored. This study assesses the genetic diversity of A. monoceros along the Indian coastline using mitochondrial DNA markers. The analysis revealed high haplotype diversity, indicating considerable genetic variation within the species. Results from the Analysis of Molecular Variance (AMOVA) showed minimal genetic differentiation among populations. Low ΦST values suggested extensive gene flow among populations across the Indian coast. Neutrality tests further indicated signals of recent population expansions or selective sweeps. This study provides baseline information on the genetic diversity and population structure of A. monoceros, supporting the existence of a predominantly panmictic population with minor regional variation. The findings highlight the feasibility of managing populations along the Indian coast as a single genetic management unit.","PeriodicalId":74204,"journal":{"name":"Mitochondrial DNA. Part A, DNA mapping, sequencing, and analysis","volume":" ","pages":"207-213"},"PeriodicalIF":0.6,"publicationDate":"2025-10-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145350316","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 chloroplast genome sequences and phylogenetics of Cornus sanguinea L. and Cornus sericea L. (Cornaceae). 山茱萸和山茱萸叶绿体全基因组序列及系统发育。

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Mitochondrial DNA. Part A, DNA mapping, sequencing, and analysis Pub Date : 2025-10-01 Epub Date: 2025-11-09 DOI: 10.1080/24701394.2025.2584519

Eugenia Nikonorova, Alexandr Shevtsov, Nailya Tursunbay, Oxana Khapilina, Dmitry Baleev

{"title":"The complete chloroplast genome sequences and phylogenetics of Cornus sanguinea L. and Cornus sericea L. (Cornaceae).","authors":"Eugenia Nikonorova, Alexandr Shevtsov, Nailya Tursunbay, Oxana Khapilina, Dmitry Baleev","doi":"10.1080/24701394.2025.2584519","DOIUrl":"10.1080/24701394.2025.2584519","url":null,"abstract":"This study presents a comprehensive analysis of the chloroplast genomes of two species belonging to the genus Cornus, Cornus sanguinea L. and Cornus sericea L. Both plastomes exhibit a typical circular quadripartite structure, with slight variations in the lengths of the large and small single-copy regions. The complete chloroplast genomes of C. sericea and C. sanguinea were assembled and characterized, with lengths of 158,244 bp and 158,663 bp, respectively. A total of 131 genes were identified in each cp genome, comprising 86 protein-coding genes, 37 transfer RNA (tRNA) genes, and 8 ribosomal RNA (rRNA) genes. Notably, tetra-, penta-, and hexa-nucleotide simple sequence repeats were absent in both genomes. We investigated the taxonomic relationships among the Cornaceae and the closely related families Hydrangeaceae, Nyssaceae, Garryaceae, Curtisiaceae, and Grubbiaceae. Phylogenetic analyses clustered C. sanguinea and C. sericea into a single well-supported clade Cornaceae, reflecting their close relationships with other species in the family, which is consistent with previous studies. Overall, this study provides new insights into the structure and features of the C. sericea and C. sanguinea cp genomes.","PeriodicalId":74204,"journal":{"name":"Mitochondrial DNA. Part A, DNA mapping, sequencing, and analysis","volume":" ","pages":"222-230"},"PeriodicalIF":0.6,"publicationDate":"2025-10-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145484038","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

Excess of non-synonymous mutations and structural variations in mitogenomes of freshwater snails in the genus Semisulcospira. 半螺属淡水蜗牛有丝分裂基因组的非同义突变和结构变异。

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Mitochondrial DNA. Part A, DNA mapping, sequencing, and analysis Pub Date : 2025-10-01 Epub Date: 2025-11-05 DOI: 10.1080/24701394.2025.2583076

Himeka Kawabata, Osamu Miura

{"title":"Excess of non-synonymous mutations and structural variations in mitogenomes of freshwater snails in the genus Semisulcospira.","authors":"Himeka Kawabata, Osamu Miura","doi":"10.1080/24701394.2025.2583076","DOIUrl":"10.1080/24701394.2025.2583076","url":null,"abstract":"Mitochondrial DNA has unique biological characteristics, such as a high mutation rate and clonal inheritance, which make it an appropriate marker in molecular biology. However, exceptionally high mitochondrial divergences have been reported in terrestrial and marine invertebrates, plants, and certain vertebrate lineages, which complicates the interpretation of the results in DNA barcoding and evolutionary studies. The freshwater snails in the genus Semisulcospira have two mitochondrial DNA lineages: a normal mitochondrial lineage (mt-A type) and a highly divergent 'enigmatic' lineage (mt-B type). We assembled thirty-two mitogenomes of Semisulcospira to understand the molecular evolution of the mt-B type. We found that the mt-B type evolves faster than the mt-A type, has more non-synonymous mutations, and exhibits structural variations with truncated cob and cox3 genes. Our results showed that the observed molecular evolution of the mt-B type could result from a decreased efficiency of natural selection due to small population size and/or the accumulation of slightly deleterious mutations caused by mitochondrial sex ratio distortion.","PeriodicalId":74204,"journal":{"name":"Mitochondrial DNA. Part A, DNA mapping, sequencing, and analysis","volume":" ","pages":"214-221"},"PeriodicalIF":0.6,"publicationDate":"2025-10-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145454136","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. 修正。

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Mitochondrial DNA. Part A, DNA mapping, sequencing, and analysis Pub Date : 2025-10-01 Epub Date: 2025-11-18 DOI: 10.1080/24701394.2025.2585421

引用次数: 0