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

Little variation, lots of repetition: mitogenomic diversity in African wild dogs. 变异少，重复多：非洲野狗的有丝分裂基因组多样性。

IF 0.6

Mitochondrial DNA. Part A, DNA mapping, sequencing, and analysis Pub Date : 2025-09-11 DOI: 10.1080/24701394.2025.2558612

Laura Tensen, Bettine Jansen van Vuuren, Rosemary Groom, Cole du Plessis, Klaus Fischer

{"title":"Little variation, lots of repetition: mitogenomic diversity in African wild dogs.","authors":"Laura Tensen, Bettine Jansen van Vuuren, Rosemary Groom, Cole du Plessis, Klaus Fischer","doi":"10.1080/24701394.2025.2558612","DOIUrl":"https://doi.org/10.1080/24701394.2025.2558612","url":null,"abstract":"African wild dogs (Lycaon pictus) are the sole representative of their genus, and form an ancestral lineage most closely related to Asian dholes (Cuon alpinus) and Ethiopian wolves (Canis simensis). They suffered tremendous demographic losses over the past decades and have low levels of mitochondrial (mtDNA) variation, previously measured with a 381 bp segment of the Control region (CR). In this study, we did a whole mitochondrial genome (mitogenomes) comparison of 20 wild dogs from South Africa and Zimbabwe. We questioned (i) whether low levels of mtDNA diversity (typically seen in the CR) are also observed in other regions of the mitogenome, (ii) how mitogenomic diversity in wild dogs compares to other species, and (iii) how mitogenomic lineages have diverged across time. We found that mtDNA diversity was low across the genome, with 5 unique haplotypes across 16,829-17,531 bp (and only 11 CR haplotypes across their entire range), and a nucleotide diversity (π) of 0.0009, which is much lower than most other animal species. We also found an imperfect tandem repeat ('ACACATACGT') at the flanks of the CR, with a total length that extends much further than typically observed in animals, varying between 43-989 bp among individuals. Because the CR is noncoding, this may have occurred due to DNA slippage in a lack of selective constraints. The low number of haplotypes may be the effect of historic population contractions and recent demographic losses, which wild dogs are known to have experienced.","PeriodicalId":74204,"journal":{"name":"Mitochondrial DNA. Part A, DNA mapping, sequencing, and analysis","volume":" ","pages":"1-10"},"PeriodicalIF":0.6,"publicationDate":"2025-09-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145034887","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

Comparative mitogenomics of the eulipotyphlan species (Mammalia, Eulipotyphla) provides novel insights into the molecular evolution of hibernation. 真丝虫物种（哺乳动物，真丝虫）的比较有丝分裂基因组学为冬眠的分子进化提供了新的见解。

IF 0.6

Mitochondrial DNA. Part A, DNA mapping, sequencing, and analysis Pub Date : 2025-09-11 DOI: 10.1080/24701394.2025.2558619

Lijia Chen, Guang Yang, Simin Chai

{"title":"Comparative mitogenomics of the eulipotyphlan species (Mammalia, Eulipotyphla) provides novel insights into the molecular evolution of hibernation.","authors":"Lijia Chen, Guang Yang, Simin Chai","doi":"10.1080/24701394.2025.2558619","DOIUrl":"https://doi.org/10.1080/24701394.2025.2558619","url":null,"abstract":"Hibernation is an elaborate response strategy employed by numerous mammals to survive in cold conditions that involves active suppression of metabolism. Despite the role of mitochondria as energy metabolism centers during hibernation, the adaptive and evolutionary mechanisms of mitochondrial genes in hibernating animals, like hedgehogs in eulipotyphlan species, are not yet fully understood. In this study, we sequenced and assembled mitochondrial genomes of the hibernating four-toed hedgehog (Atelerix albiventris) and the non-hibernating Asian house shrew (Suncus murinus). While no significant positive selection was detected, we identified unique amino acid substitutions and accelerated evolutionary rates of mitochondrial proteins and the encoding genes in hibernating hedgehogs. Moreover, the distinctive evolutionary patterns indicated a potential link among the adaptive evolution of mitochondrial genes (such as ATP6, CYTB, and ND6), the phenotypes of hibernation and longevity in eulipotyphlan species. These three genes evolved rapidly in hibernating Erinaceidae species and exhibited significant correlations with the two distinct phenotypes, indicating their pivotal roles in the evolution of hibernation and longevity. These findings provide insights into the genetic mechanisms responsible for metabolic plasticity and longevity in eulipotyphlan hibernators, with implications for other mammalian taxa.","PeriodicalId":74204,"journal":{"name":"Mitochondrial DNA. Part A, DNA mapping, sequencing, and analysis","volume":" ","pages":"1-13"},"PeriodicalIF":0.6,"publicationDate":"2025-09-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145034826","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

Insights into traditional Chinese medicine: molecular identification of black-spotted tokay gecko, Gekko reevesii, and related species used as counterfeits based on mitochondrial 16S rRNA gene sequences. 中药的见解：基于线粒体16S rRNA基因序列的黑斑东头壁虎、壁虎及相关假药物种的分子鉴定。

IF 0.6

Mitochondrial DNA. Part A, DNA mapping, sequencing, and analysis Pub Date : 2025-08-28 DOI: 10.1080/24701394.2025.2550967

Fuli Jiang, Linmiao Yan, Xiaotong Jing, Guangyu Chen, Yilin Wang, Chengjian Zhao, Yong Huang

{"title":"Insights into traditional Chinese medicine: molecular identification of black-spotted tokay gecko, Gekko reevesii, and related species used as counterfeits based on mitochondrial 16S rRNA gene sequences.","authors":"Fuli Jiang, Linmiao Yan, Xiaotong Jing, Guangyu Chen, Yilin Wang, Chengjian Zhao, Yong Huang","doi":"10.1080/24701394.2025.2550967","DOIUrl":"https://doi.org/10.1080/24701394.2025.2550967","url":null,"abstract":"Authentication of traditional Chinese medicine (TCM) is challenging due to DNA degradation in Chinese medicinal materials, which are usually processed and stored dry. The standard DNA barcoding length (648 bp) or longer are difficult to amplify, which makes it difficult to identify adulterants in Chinese medicinal materials. In this study, we used the mitochondrial 16S rRNA gene (< 200bp) as a barcode to differentiate black-spotted tokay geckoes (Gekko reevesii) from the related species used as counterfeits. We collected 63 specimens from 17 species of G. reevesii and their counterfeits, and each specimen generated a 189 bp 16S rRNA gene sequence. The average uncorrected p-distances within genuine G. reevesii was 0.9%, while the average uncorrected p-distances between G. reevesii and their counterfeits was 6.3% (at a minimum). According to phylogenetic analysis and genetic distances, the genuine G. reevesii samples collected in this study constitute a monophyly that can be distinguished from its counterfeits in TCM formulations, including G. gecko (red-spotted tokay geckos), which have very similar morphology. Thus, the short 16S rRNA barcode provides an effective tool for distinguishing G. reevesii from its counterfeits, ensuring the safety and efficacy of clinical medications containing components from G. reevesii in TCM.","PeriodicalId":74204,"journal":{"name":"Mitochondrial DNA. Part A, DNA mapping, sequencing, and analysis","volume":" ","pages":"1-8"},"PeriodicalIF":0.6,"publicationDate":"2025-08-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144981626","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 of Origanum vulgare L. (Lamiaceae) from AL-Madinah, Saudi Arabia, and its phylogenetic relationship. 沙特阿拉伯AL-Madinah地区一枝牛（Origanum vulgare L.）叶绿体全基因组及其系统发育关系。

IF 0.6

Mitochondrial DNA. Part A, DNA mapping, sequencing, and analysis Pub Date : 2025-08-25 DOI: 10.1080/24701394.2025.2550936

Samaila Samaila Yaradua, Faten Zubair Filimban

{"title":"The complete chloroplast genome of Origanum vulgare L. (Lamiaceae) from AL-Madinah, Saudi Arabia, and its phylogenetic relationship.","authors":"Samaila Samaila Yaradua, Faten Zubair Filimban","doi":"10.1080/24701394.2025.2550936","DOIUrl":"https://doi.org/10.1080/24701394.2025.2550936","url":null,"abstract":"The genus Origanum is taxonomically complex and often considered an underutilized group despite its economic and medicinal significance. Origanum vulgare L., the most variable species within the genus, is widely utilized as a culinary spice and medicinal herb, exhibiting considerable morphological diversity across its six recognized subspecies. In this study, we assembled and annotated the complete chloroplast (cp) genome of a wilt-resistant Saudi Arabian accession of O. vulgare. The cp genome measures 151,826 bp in length and displays the typical circular quadripartite structure, consisting of a large single copy (LSC) region (83,014 bp), a small single copy (SSC) region (17,620 bp), and a pair of inverted repeats (IRs) (25,596 bp each). It contains 129 genes, including 85 protein-coding genes, 36 transfer RNA genes, and 8 ribosomal RNA genes. Notably, the Saudi accession possesses a duplicated rps19 gene, and its cp genome length differs from that of other O. vulgare accessions. Phylogenetic analysis clustered all O. vulgare accessions into a single well-supported clade, revealing considerable genetic divergence among populations. Furthermore, the genus Origanum was strongly supported as sister to Thymus. This study provides a valuable chloroplast genome resource for evolutionary, taxonomic, and conservation studies in O. vulgare and related taxa within the Lamiaceae.","PeriodicalId":74204,"journal":{"name":"Mitochondrial DNA. Part A, DNA mapping, sequencing, and analysis","volume":" ","pages":"1-7"},"PeriodicalIF":0.6,"publicationDate":"2025-08-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144981173","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

Genetic diversity in snakeskin gourami (Trichopodus pectoralis Regan, 1910): evaluating cultured and wild populations in Southeast Asia for breeding improvement programs. 蛇皮gourami （Trichopodus pectoralis Regan, 1910）的遗传多样性：评估东南亚养殖种群和野生种群的育种改进计划。

Mitochondrial DNA. Part A, DNA mapping, sequencing, and analysis Pub Date : 2025-06-13 DOI: 10.1080/24701394.2025.2514279

Liem Thanh Pham, Ngoc-Tran Thi Nguyen, Tam Minh Bui, Long Nhut Duong, Thuy-Yen Duong

{"title":"Genetic diversity in snakeskin gourami (Trichopodus pectoralis Regan, 1910): evaluating cultured and wild populations in Southeast Asia for breeding improvement programs.","authors":"Liem Thanh Pham, Ngoc-Tran Thi Nguyen, Tam Minh Bui, Long Nhut Duong, Thuy-Yen Duong","doi":"10.1080/24701394.2025.2514279","DOIUrl":"https://doi.org/10.1080/24701394.2025.2514279","url":null,"abstract":"Assessing genetic diversity among potential populations provides crucial insights for genetic improvement programs targeting long-domesticated fish species. In this study, we evaluated genetic diversity levels using mitochondrial control region sequences of snakeskin gourami from one cultured and two wild populations (Ca Mau, CM and Kien Giang, KG) in the Mekong Delta, Viet Nam, alongside two other wild populations from Cambodia and Thailand. A total of 128 samples yielded 46 haplotypes, with five populations collectively contributing 42 unique haplotypes. All populations exhibited relatively high levels of genetic diversity, with haplotype diversity ranging from 0.719 to 0.877 and nucleotide diversity from 0.0075 to 0.0107. Statistically significant genetic differences were detected between the cultured and wild populations (FST range: 0.205-0.313), whereas weak genetic structure was observed among wild populations along the Mekong basin. These findings suggest that the cultured population holds potential as a base for genetic improvements, but crossbreeding between genetically distinct cultured and wild stocks should be carefully evaluated before large-scale seed production.","PeriodicalId":74204,"journal":{"name":"Mitochondrial DNA. Part A, DNA mapping, sequencing, and analysis","volume":" ","pages":"1-7"},"PeriodicalIF":0.0,"publicationDate":"2025-06-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144287500","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 of the 'maze' coral Meandrina meandrites (Scleractinia: Vacatina: Meandrinidae). 迷宫珊瑚Meandrina meandrites的完整线粒体基因组（scactinia: Vacatina: Meandrinidae）。

Mitochondrial DNA. Part A, DNA mapping, sequencing, and analysis Pub Date : 2025-06-07 DOI: 10.1080/24701394.2025.2504422

J Antonio Baeza, Stephanie M Rosales

{"title":"The complete mitochondrial genome of the 'maze' coral Meandrina meandrites (Scleractinia: Vacatina: Meandrinidae).","authors":"J Antonio Baeza, Stephanie M Rosales","doi":"10.1080/24701394.2025.2504422","DOIUrl":"https://doi.org/10.1080/24701394.2025.2504422","url":null,"abstract":"The shallow water reef-building 'maze' or 'brain' stony coral Meandrina meandrites (fam. Meandrinidae) is currently experiencing major environmental problems in the Caribbean Sea. In this study, we assembled the mitochondrial genome of M. meandrites to support future conservation of this imperiled coral. We also explored the phylogenetic position of this coral in the Class Scleractinia utilizing the phylogenetic signal provided by translated mitochondrial protein-coding genes (PCGs). A complete mitochondrial genome of M. meandrites, 17,196 bp in length, was assembled using short-reads next-generation sequencing (NGS) sequencing with the target-restricted-assembly pipeline GetOrganelle. The newly assembled mitochondrial genome of M. meandrites encoded 13 PCGs, two ribosomal genes (ribosomal RNA), and two transfer genes (tRNAs). It also contains two relatively long non-coding regions 400 and 1,877 bp long. A group I intron bisected the nad5 PCG. Each of the two tRNAs exhibited a canonical 'cloverleaf' secondary structure. The mitochondrial genome of M. meandrites is identical to that of a conspecific assembled using HiFi PacBio long reads (available in GenBank with accession number OY855917 but without a companion paper) with the exception of four single nucleotide variants. The aforementioned comparison indicates that the mitochondrial genome assembled from a short-read NGS dataset is reliable (complete and accurate). A maximum-likelihood phylomitogenomic analysis based on PCGs (translated) supported the monophyly of the order Scleractinia and placed M. meandrites in a moderately to well-supported clade with Astrangia sp. (family Astrangidae). This newly assembled mitochondrial genome can be used as a reference to support conservation planning, including biomonitoring of this stony coral using environmental DNA.","PeriodicalId":74204,"journal":{"name":"Mitochondrial DNA. Part A, DNA mapping, sequencing, and analysis","volume":" ","pages":"1-8"},"PeriodicalIF":0.0,"publicationDate":"2025-06-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144251188","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

A cryptic species of the nemertean egg predator Carcinonemertes conanobrieni (Simpson et al., 2017) detected using a barcoding approach infects the Caribbean spiny lobster Panulirus argus (Latreille, 1804) in the southwestern Caribbean Sea. 使用条形码方法检测到的一种隐种nemertean卵捕食者Carcinonemertes conanobrieni （Simpson et al., 2017）感染了加勒比海西南部的加勒比刺龙虾Panulirus argus （Latreille, 1804）。

Mitochondrial DNA. Part A, DNA mapping, sequencing, and analysis Pub Date : 2025-05-04 DOI: 10.1080/24701394.2025.2499461

J Antonio Baeza, Rodolfo Umaña-Castro, Donald C Behringer, Arcadio Castillo

{"title":"A cryptic species of the nemertean egg predator Carcinonemertes conanobrieni (Simpson et al., 2017) detected using a barcoding approach infects the Caribbean spiny lobster Panulirus argus (Latreille, 1804) in the southwestern Caribbean Sea.","authors":"J Antonio Baeza, Rodolfo Umaña-Castro, Donald C Behringer, Arcadio Castillo","doi":"10.1080/24701394.2025.2499461","DOIUrl":"https://doi.org/10.1080/24701394.2025.2499461","url":null,"abstract":"A recently discovered nemertean egg predator, Carcinonemertes conanobrieni, inhabiting Panulirus argus egg masses poses a potential threat to this ecologically and commercially relevant lobster. This study assessed the prevalence of C. conanobrieni in the southwestern Caribbean Sea; Costa Rica and Panama. Brooding females of P. argus were collected by fishermen near Punta Uva beach, Costa Rica (n = 17), and Guna Yala, Panama (n = 19) and examined for the presence of C. conanobrieni. Prevalence of C. conanobrieni in brooding lobsters, determined as the presence/absence of adults, juveniles, encysted juvenile worms, or carcinonemertid egg masses was 47.06% and 31.58% in Costa Rica and Panama, respectively. Moreover, when indirect evidence (empty capsules and/or dead embryos presumably attacked/consumed by worms) of the presence of C. conanobrieni in brooding lobsters is considered in addition to direct evidence, prevalence of C. conanobrieni in brooding lobsters was 64.71% and 47.37% in Costa Rica and Panama, respectively. The observations suggest that this parasitic worm completes its life cycle locally in the southwestern Caribbean. Notably, a Maximum Likelihood phylogenetic analysis based on a fragment of the mitochondrial cox1 gene clustered two specimens collected in Costa Rica together with four other specimens previously collected in Saint Kitts into a single fully supported monophyletic clade that segregated from a second clade containing six specimens of C. conanobrieni collected in Colombia, Florida, and Saint Kitts. The barcoding analysis suggests that there is an undescribed species of Carcinonemertes, anatomically like C. conanobrieni, infecting P. argus in Costa Rica.","PeriodicalId":74204,"journal":{"name":"Mitochondrial DNA. Part A, DNA mapping, sequencing, and analysis","volume":" ","pages":"1-6"},"PeriodicalIF":0.0,"publicationDate":"2025-05-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143999670","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

General features and evolution of mitochondrial genomes in Dictyostelia (Amoebozoa). 双壳类动物（变形虫）线粒体基因组的一般特征和进化。

Mitochondrial DNA. Part A, DNA mapping, sequencing, and analysis Pub Date : 2025-04-07 DOI: 10.1080/24701394.2025.2487451

Kamonchat Prommarit, Thanyaporn Chittavichai, Supanut Utthiya, Sukhita Sathitnaitham, Supachai Vuttipongchaikij, Passorn Wonnapinij

{"title":"General features and evolution of mitochondrial genomes in Dictyostelia (Amoebozoa).","authors":"Kamonchat Prommarit, Thanyaporn Chittavichai, Supanut Utthiya, Sukhita Sathitnaitham, Supachai Vuttipongchaikij, Passorn Wonnapinij","doi":"10.1080/24701394.2025.2487451","DOIUrl":"https://doi.org/10.1080/24701394.2025.2487451","url":null,"abstract":"Dictyostelia exhibits high diversity; however, mitochondrial genome data remain scarce for many genera. Although key features of some dictyostelid mitogenomes have been identified, several aspects remain unclear, including core gene content, segmental arrangement, and differences between 18S rRNA and mitochondrial gene phylogenies. To address these gaps, we reconstructed two complete mitogenomes-from Cavenderia subdiscoidea and Dictyostelium sp. (TH18CC)-and analyzed mitochondrial genes from ten genera and six additional complete mitogenomes from public databases. A comparison of eight complete mitogenomes revealed a conserved core of 39 protein-coding genes, 17 tRNA genes, and three rRNA genes. Two distinct segmental arrangements were identified: Dictyostelium (except D. purpureum) exhibits an A-C-B pattern, while other genera display an A-B-C pattern defined by the clusters nad9-atp1, trnC(GCA)-atp9, and rnl-nad3. Phylogenetic analyses based on 18S rDNA and mitochondrial rns suggest the transposition between segments B and C occurred after D. purpureum diverged from other Dictyostelium species, potentially involving tRNA gene displacement. In contrast, the mitochondrial protein-coding gene phylogeny differs from the rRNA trees, indicating that these gene sets may have evolved independently. These findings advance our understanding of dictyostelid mitogenome structure and evolution.","PeriodicalId":74204,"journal":{"name":"Mitochondrial DNA. Part A, DNA mapping, sequencing, and analysis","volume":" ","pages":"1-13"},"PeriodicalIF":0.0,"publicationDate":"2025-04-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143804959","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

Genetic diversity, population genetic structure and demographic history of the Ribbontail stingray Taeniura lymma (Fabricius, 1775) (elasmobranchii: myliobatiformes: dasyatidae) along the Tanzanian coastline. 坦桑尼亚海岸线带尾黄貂鱼 Taeniura lymma (Fabricius, 1775) (elasmobranchii: myliobatiformes: dasyatidae) 的遗传多样性、种群遗传结构和人口历史。

Mitochondrial DNA. Part A, DNA mapping, sequencing, and analysis Pub Date : 2025-04-01 Epub Date: 2024-11-18 DOI: 10.1080/24701394.2024.2427841

Alex Nehemia

{"title":"Genetic diversity, population genetic structure and demographic history of the Ribbontail stingray Taeniura lymma (Fabricius, 1775) (elasmobranchii: myliobatiformes: dasyatidae) along the Tanzanian coastline.","authors":"Alex Nehemia","doi":"10.1080/24701394.2024.2427841","DOIUrl":"10.1080/24701394.2024.2427841","url":null,"abstract":"The Ribbontail stingray Taeniura lymma is an economically important fish and attractive species for the aquarium trade industry. Overfishing, habitat degradation, and pollution, however, pose a threat to this species. This study used partial mitochondrial cytochrome oxidase subunit I (COI) sequences (603 base pairs long) from 96 samples of T. lymma collected at five fish-landing sites (Deep Sea-Tanga, Malindi-Unguja, Kaole-Bagamoyo, Kivukoni-Dar es Salaam, and Bandarini-Mtwara) located along the coast of Tanzania to determine the species' genetic diversity, population genetic structure, and demographic history. The findings revealed an average nucleotide diversity of 0.24 ± 0.16% and a haplotype diversity of 0.75 ± 0.04. Nucleotide and haplotype diversities were relatively low at Kaole-Bagamoyo compared to the other studied localities. An Analysis of Molecular Variance (AMOVA) indicated limited but statistically significant genetic differences among populations (Overall FST = 0.09, p < 0.01). Pairwise AMOVA revealed genetic difference between the Deep Sea-Tanga population and all other populations studied with exception of Malindi-Unguja. Analyses of mismatch distribution, demographic history, and a haplotype network support a scenario of historical population expansion in the studied species. Immediate effort is required to protect population exhibiting low genetic diversity in this commercially important ray.","PeriodicalId":74204,"journal":{"name":"Mitochondrial DNA. Part A, DNA mapping, sequencing, and analysis","volume":" ","pages":"93-101"},"PeriodicalIF":0.0,"publicationDate":"2025-04-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142649609","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

Description and characterization of the small mitochondrial genome of Trichoderma cerinum (Hypocreales, Hypocreaceae) and its evolutionary perspectives. 陶瓷毛霉（Hypocreales，Hypocreaceae）小线粒体基因组的描述和特征及其进化前景。

Mitochondrial DNA. Part A, DNA mapping, sequencing, and analysis Pub Date : 2025-04-01 Epub Date: 2025-03-21 DOI: 10.1080/24701394.2025.2482202

Priscila Martins de Assis, Igor Henrique Rodrigues-Oliveira, Iuri Batista da Silva, Rubens Pasa, Fabiano B Menegidio, Karine Frehner Kavalco

{"title":"Description and characterization of the small mitochondrial genome of Trichoderma cerinum (Hypocreales, Hypocreaceae) and its evolutionary perspectives.","authors":"Priscila Martins de Assis, Igor Henrique Rodrigues-Oliveira, Iuri Batista da Silva, Rubens Pasa, Fabiano B Menegidio, Karine Frehner Kavalco","doi":"10.1080/24701394.2025.2482202","DOIUrl":"10.1080/24701394.2025.2482202","url":null,"abstract":"Trichoderma Persoon (1794) is a genus of fungus found in soils and decaying wood all over the world. We present the assembly and annotation of the mitochondrial genome of Trichoderma cerinum Bissett, Kubicek & Szakacs (2003) and an assessment of the phylogeny of the group, discussing the loss and gain of shared genes in the evolutionary history of fungi. We downloaded the raw data of T. cerinum from the NCBI database and exported it to the Galaxy Europe platform, where we performed the mitogenome assembly using the NOVOplasty tool. We used three tools for annotation. The phylogeny was conducted with 12 Trichoderma species and the T. cerinum. Fusarium oxysporum was used as an outgroup. We got a circularized mitochondrial genome of 26,696 bp, with 15 protein-coding genes, 25 tRNAs, two rRNAs, two endonuclease sequences, and an orf40. This species contains only one intron in the cob gene. In our phylogenetic reconstruction, T. cerinum was recovered as a sister group of a clade containing Trichoderma lixii, Trichoderma afroharzianum, Trichoderma simmonsii, and Trichoderma harzianum.","PeriodicalId":74204,"journal":{"name":"Mitochondrial DNA. Part A, DNA mapping, sequencing, and analysis","volume":" ","pages":"126-134"},"PeriodicalIF":0.0,"publicationDate":"2025-04-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143674999","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