Suvi Olli, Nok Ting Lam, Siri Hiljanen, Taru Kettunen, Laura Haikonen, Heidi-Mari Hyvönen, Angelika Kiebler, Ida Köngäs, Saana Minkkinen, Veera Pöykiö, Ville Sannikka, Ronja Vesa, Gerrit Wehrenberg, Stefan Prost, Marko Prous
{"title":"Large mitochondrial genomes in tenthredinid sawflies (Hymenoptera, Tenthredinidae).","authors":"Suvi Olli, Nok Ting Lam, Siri Hiljanen, Taru Kettunen, Laura Haikonen, Heidi-Mari Hyvönen, Angelika Kiebler, Ida Köngäs, Saana Minkkinen, Veera Pöykiö, Ville Sannikka, Ronja Vesa, Gerrit Wehrenberg, Stefan Prost, Marko Prous","doi":"10.1080/24701394.2024.2427206","DOIUrl":"https://doi.org/10.1080/24701394.2024.2427206","url":null,"abstract":"<p><p>We sequenced and assembled mitochondrial genomes of three tenthredinid sawflies (<i>Euura poecilonota</i>, <i>E. striata</i>, and <i>Dolerus timidus</i>) using Oxford Nanopore Technologies' MinION. The Canu assembler produced circular assemblies (23,000-40,000 bp). Still, errors were found in the highly repetitive non-coding control region because of the fragmented DNA which led to no reads spanning the complete control region, preventing its reliable assembly. Based on the non-repetitive coding region's sequencing coverage, we estimate the lengths of mitochondrial genomes of <i>E. poecilonota</i>, <i>D. timidus</i>, and <i>E. striata</i> to be about 30,000 bp, 31,000 bp, and 37,000 bp and control region to be 15,000 bp, 16,000 bp, and 22,000 bp respectively. All standard bilaterian mitochondrial genes are in the same order and orientation, except <i>trnQ</i>, which is on the minus strand in <i>Euura</i> and the plus strand in <i>Dolerus</i>. Using published tenthredinid genome data, we show that control region lengths are often underestimated.</p>","PeriodicalId":74204,"journal":{"name":"Mitochondrial DNA. Part A, DNA mapping, sequencing, and analysis","volume":" ","pages":"1-9"},"PeriodicalIF":0.0,"publicationDate":"2024-11-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142633907","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":"Comparative selective pressure analysis on mitochondrial protein-coding genes in flying squirrels (Pteromyini) and tree squirrels (Sciurini).","authors":"Feiyun Tu, Yaqin Qiao, Wenjing Zhao, Tong Wu","doi":"10.1080/24701394.2024.2416179","DOIUrl":"https://doi.org/10.1080/24701394.2024.2416179","url":null,"abstract":"<p><p>Different animal groups with varying locomotion modes may have unique energy requirements. Mitochondria produce adenosine triphosphate (ATP) and reactive oxygen species via oxidative phosphorylation to support organisms energy requirements. The tribes Pteromyini (flying squirrels) and Sciurini (tree squirrels), two closely related taxa within the family Sciuridae, exhibit distinct locomotion modes, energy requirements, and likely face different selective pressures on mitochondrial protein-coding genes (PCGs). We analysed 13 mitochondrial genome sequences from species belonging to the tribe Pteromyini and 117 from species belonging to the tribe Sciurini. Phylogenetic analysis revealed Pteromyini and Sciurini formed a sister relationship within the family Sciuridae. Among the 13 PCGs, <i>ATP8</i> exhibited the highest dN/dS values, while <i>COX1</i> showed the lowest. The background selection ratio (ω<sub>2</sub>) values for six genes (<i>ND1</i>, <i>ND2</i>, <i>ND4</i>, <i>ATP6</i>, <i>ND5</i>, and <i>COX3</i>) in Pteromyini were lower than the foreground selection ratio (ω<sub>0</sub>) values observed in Sciurini. A RELAX analysis revealed that <i>CYTB</i>, <i>ND4</i>, <i>ATP6</i>, and <i>COX3</i> genes experienced intensified in selection strength. BUSTED analysis identified stronger signatures of diversifying selection in <i>CYTB</i> and <i>ATP6</i>, highlighting amino acid changes. MEME identified episodic diversifying selection at specific sites among eight PCGs. These findings revealed distinct selective pressures on PCGs in flying and tree squirrels.</p>","PeriodicalId":74204,"journal":{"name":"Mitochondrial DNA. Part A, DNA mapping, sequencing, and analysis","volume":" ","pages":"1-9"},"PeriodicalIF":0.0,"publicationDate":"2024-10-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142482475","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}
Sandra Ludwig, Lais Amorim, Ana C Barcelos, Paula R Guimarães, Sarah M Vargas
{"title":"Inferring the origin of new D-loop haplotypes of loggerhead sea turtles (Testudinata: Cheloniidae) from the Southwest Atlantic lineage.","authors":"Sandra Ludwig, Lais Amorim, Ana C Barcelos, Paula R Guimarães, Sarah M Vargas","doi":"10.1080/24701394.2024.2409067","DOIUrl":"https://doi.org/10.1080/24701394.2024.2409067","url":null,"abstract":"<p><p>The populations of the loggerhead turtles, <i>Caretta caretta,</i> present four main D-loop mitochondrial haplogroups that are distributed across the Indo-Pacific, Mediterranean, and Atlantic oceans. The Southwestern Atlantic (SWA) is one of the Regional Management Units (RMUs) of loggerheads, characterized by unique haplotypes, high nest density, and distinct life history traits. Detecting new D-loop haplogroups is important, particularly endemic ones, as they can enhance our understanding of their life history within the RMUs and contribute to the resolution of mixed stock analysis. In this study, we conducted a series of phylogenetic delimitation and network analyses to identify, validate, and infer the origin of four new D-loop haplotypes detected in the loggerhead populations from the SWA. Our findings demonstrate that these new D-loop haplotypes are valid and unique to the SWA lineage, potentially aiding in the delimitation of individuals' origins and the inference of their lineage.</p>","PeriodicalId":74204,"journal":{"name":"Mitochondrial DNA. Part A, DNA mapping, sequencing, and analysis","volume":" ","pages":"1-8"},"PeriodicalIF":0.0,"publicationDate":"2024-09-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142333936","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":"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}
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 <i>Odontomachus</i> (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":"<p><p>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 <i>Odontomachus</i>. Our data reveal a gene duplication event in Formicidae, the first involving <i>trnV</i>, and new gene arrangements involving the <i>trnM-trnI-trnQ</i> and <i>trnW-trnC-trnY</i> 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 <i>Odontomachus</i> and <i>Pachycondyla</i>.</p>","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}
{"title":"The complete mitochondrial genome and phylogenetic position of <i>Schizothorax argentatus</i> (Cyprinomorpha: Crypriniformes: Cyprinidae).","authors":"Zhengduan Huang, Dilina Rusitanmu, Jie Han","doi":"","DOIUrl":"","url":null,"abstract":"<p><p>We investigated the vulnerable fish species <i>Schizothorax argentatus</i> Kessler, 1874, using low-coverage whole genome sequencing data. The assembled 16,587 bp mitochondrial genome has a nucleotide composition of A = 29.8%, T = 25.3%, G = 17.9%, and C = 27.0%, containing 13 protein-coding genes, two ribosomal RNA genes, and 22 transfer RNA genes with a gene arrangement identical to other cofamilial species. Phylogenetic analyses of 71 schizothoracine fishes suggest a close relationship between <i>S. argentatus</i> and <i>Schizothorax eurystomus</i>, sharing a common ancestor with <i>Schizothorax pseudoaksaiensis</i>. Our study supports dividing extant schizothoracine fishes into two tribes, Schizothoracini and Schizopygopsini. The estimated time to most recent common ancestor (<i>t<sub>MRCA</sub></i>) and their distribution imply geological and climatic events during the Miocene around the Qinghai-Tibet Plateau as significant evolutionary drivers explaining the diversification of main clades in schizothoracine fishes.</p>","PeriodicalId":74204,"journal":{"name":"Mitochondrial DNA. Part A, DNA mapping, sequencing, and analysis","volume":" ","pages":"1-9"},"PeriodicalIF":0.0,"publicationDate":"2024-03-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140095333","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}
Kavita Kumari, Simanku Borah, Sangeetha M Nair, Vettath Raghavan Suresh
{"title":"<i>Opsarius siangi</i>, 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":"<p><p><i>Opsarius siangi</i> 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 <i>Opsarius</i> and <i>Barilius</i> genera. Phylogenetic analysis revealed that <i>O. siangi</i> sp. nov. occupies a distinctive clade, displaying close affinity with <i>O. shacra</i>. Intraspecific K2P genetic divergence, assessed at 0.02, falls well within established species delineation thresholds, while interspecific divergence in comparison to <i>O. shacra</i> was recorded at 0.112. Complementary species delimitation methodologies, including BIN and bPTP, further underscore taxonomic uniqueness of <i>O. siangi</i> 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.</p>","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}
{"title":"Association between mitochondrial DNA genotype and sperm motility in humans.","authors":"Xueyou Song, Xiaoning Hong, Zilong Wang, Fuding Lu, Changze Song, Xinkun Wang, Xiaoyong Zhan, Jiaying Yu, Jiawen Zhai, Jiang Li, Xi Xiang, Xujun Xuan","doi":"10.1080/24701394.2024.2361609","DOIUrl":"10.1080/24701394.2024.2361609","url":null,"abstract":"<p><p>The relationship between genetic alterations in mitochondrial DNA (mtDNA) and progressive motility (PR) and rapid progressive motility (grade A) of ejaculated human spermatozoa remains unclear. In this study, we explored the association between human mtDNA genotype and sperm PR and grade A by analyzing mtDNA copy number, loci, haplogroup, rearrangement, deletions, and duplications and sperm motility parameters. Human sperm mtDNA copy number, loci and haplogroups were not associated with human sperm motility PR or A grade. However, the cumulative frequency of human sperm mtDNA rearrangements (including deletions and duplications) in participants with high PR and grade A ratio was higher than in participants with low PR and grade A ratio. Additional studies are needed to understand the relationship between mtDNA genotypes, including deletions and duplications, and human sperm motility.</p>","PeriodicalId":74204,"journal":{"name":"Mitochondrial DNA. Part A, DNA mapping, sequencing, and analysis","volume":" ","pages":"41-48"},"PeriodicalIF":0.0,"publicationDate":"2023-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141443882","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":"Correction.","authors":"","doi":"10.1080/24701394.2024.2348847","DOIUrl":"https://doi.org/10.1080/24701394.2024.2348847","url":null,"abstract":"","PeriodicalId":74204,"journal":{"name":"Mitochondrial DNA. Part A, DNA mapping, sequencing, and analysis","volume":"34 1-8","pages":"I"},"PeriodicalIF":0.0,"publicationDate":"2023-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143061668","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":"Mitogenomic analysis of Rüppell's fox (<i>Vulpes rueppellii</i>) confirms phylogenetic placement within the Palaearctic clade shared with its sister species, the red fox (<i>Vulpes vulpes</i>).","authors":"Ali Elsayed Basuony, Mostafa Saleh, Frank Hailer","doi":"10.1080/24701394.2024.2332320","DOIUrl":"10.1080/24701394.2024.2332320","url":null,"abstract":"<p><p>The Rüppell's fox (<i>Vulpes rueppellii</i>) 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, <i>V. vulpes</i>, remain unclear. We here report the sequencing and de-novo assembly of the first annotated mitogenome of <i>V. rueppellii</i>, analysed with data from other foxes (tribe Vulpini, subfamily Caninae). We used four bioinformatic approaches to reconstruct the <i>V. rueppellii</i> 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 <i>V. vulpes</i>. We found high support for clustering of both known subclades of <i>V. rueppellii</i> within the Palearctic clade of <i>V. vulpes</i>, 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.</p>","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}