Mitochondrial DNA. Part B, Resources最新文献

{"title":"The complete mitochondrial genome of <i>Phyllobrotica signata</i> (Mannerheim, 1825) (Coleoptera: Chrysomelidae: Galerucinae): characterization and phylogenetic implications.","authors":"Xiao-Xuan Yu, Xu Jin, Xiao-Ling Lin, Li-Na Liu, Rui-E Nie","doi":"10.1080/23802359.2024.2439465","DOIUrl":"10.1080/23802359.2024.2439465","url":null,"abstract":"<p><p>The leaf beetles have important economic and ecological significance. <i>Phyllobrotica</i> <i>signata</i> belongs to the subfamily Galerucinae. In this study, the complete mitogenome of <i>P. signata</i> has been obtained by the next-generation sequencing. The length of the new complete mitogenome is 16,207 bp containing 37 genes and a control region. Fourteen species from Galerucinae and Alticinae were selected as ingroups for phylogenetic analysis based on mitogenomic data. The results supported that <i>P. signata and P. quadrimaculata</i> were sister groups. The mitochondrial genome of P. signata will provide valuable genetic information for exploring the phylogenetic relationships in the family Chrysomelidae.</p>","PeriodicalId":18647,"journal":{"name":"Mitochondrial DNA. Part B, Resources","volume":"9 12","pages":"1688-1692"},"PeriodicalIF":0.5,"publicationDate":"2024-12-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11648148/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142837801","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"The complete mitochondrial genome of <i>Vaccinium oldhamii</i> Miquel, a plant of the Ericaceae family.","authors":"Da Hyun Lee, Woo Hyun Sim, Chung Youl Park, Do Hyun Kim, Jun Hyeok Kim, Hyeon Min Kim, Sang Hoon Che, Wan Geun Park, Chae Sun Na, Sangrea Shim","doi":"10.1080/23802359.2024.2438293","DOIUrl":"10.1080/23802359.2024.2438293","url":null,"abstract":"<p><p><i>Vaccinium oldhamii Miquel</i> 1866 is a deciduous shrub native to Northeast Asia, including Korea, China, and Japan<i>.</i> Its polyphenol-rich edible berries may aid in managing chronic diseases. Despite its importance, the mitogenome of this species remains understudied. This study assembled the complete mitogenome, consisting of 626,941 bp with 45.34% GC content, using NOVOPlasty and Illumina sequencing. The genome includes 38 protein-coding genes, 24 tRNA genes, and three rRNA genes. Phylogenetic analysis revealed a close relationship with <i>V. macrocarpon.</i> This mitogenome provides a valuable resource for phylogenomic studies and insights into evolutionary relationships within the <i>Vaccinium genus</i> and the Ericales order<i>. Vaccinium oldhamii</i> Miquel 1866 is a deciduous shrub in the Ericales and the Ericaceae and is native to Northeast Asia including Korea, China, and Japan. Particular emphasis has been placed on the edible berries of <i>Vaccinium</i> species and their use as dietary supplements. Specifically, the edible berries of <i>V. oldhamii</i> contain high levels of polyphenols, which may aid in preventing and managing chronic diseases. However, the mitogenome sequence of this species, a valuable resource for studying evolutionary relationships and genetic diversity within the <i>Vaccinium</i> genus, has not been thoroughly investigated. In this study, the complete mitochondrial genome sequence of <i>V. oldhamii</i> was assembled into 626,941 bp circular nucleotides with a GC content of 45.34% using NOVOPlasty and Illumina sequencing data. The comprehensive annotation for mitogenome of <i>V. oldhamii</i> revealed that the mitogenome comprises 38 known protein-coding genes, 24 tRNA genes, and three rRNA genes. Phylogenetic analysis using ML method showed that this species is closely related to the <i>V. macrocarpon</i>. This newly sequenced mitochondrial genome offers a valuable resource for phylogenomic analysis and will enhance our understanding of evolutionary relationships within the Ericales order and/or the <i>Vaccinium</i> genus.</p>","PeriodicalId":18647,"journal":{"name":"Mitochondrial DNA. Part B, Resources","volume":"9 12","pages":"1683-1687"},"PeriodicalIF":0.5,"publicationDate":"2024-12-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11648146/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142837803","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"The complete chloroplast genome and phylogenetic analysis of a rare species <i>Schisandra macrocarpa</i> (Schisandraceae).","authors":"Huanhuan Chen, Nawaz Haider Bashir, Lei Zhu, Tong-Xing Zhao, Tao Xu, Yong Gao, Yong-Kang Sima","doi":"10.1080/23802359.2024.2437099","DOIUrl":"10.1080/23802359.2024.2437099","url":null,"abstract":"<p><p><i>Schisandra macrocarpa</i> Lin & Shui, 2011, belongs to the family Schisandraceae and was recently added to the List of National Key Protected Wild Plants in China. We report the complete chloroplast (cp) genome of <i>S. macrocarpa</i> using Illumina Nova-Seq 6000 platform. The results showed that the cp genome size of <i>S. macrocarpa</i> was 144,288 bp, which contained a small single-copy (SSC) region (17,862 bp), a large single-copy (LSC) region (93,332 bp), and a pair of inverted repeat (IR) regions (16,547 bp). The cp genome has 40% overall GC content. Annotated genes were 128 in all, including 83 protein-coding genes, eight rRNA genes, and 37 tRNA genes. The phylogenetic analysis showed that <i>S. macrocarpa</i> was closely related to <i>S. propinqua</i> subsp<i>. sinensis</i>. This work contributes to the conservation of this species and the evolutionary analysis of Schisandraceae.</p>","PeriodicalId":18647,"journal":{"name":"Mitochondrial DNA. Part B, Resources","volume":"9 12","pages":"1693-1697"},"PeriodicalIF":0.5,"publicationDate":"2024-12-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11648132/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142837799","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Characterization and phylogenetic analysis of the complete chloroplast genome sequence of <i>Dendrobium hainanense</i> (Orchidaceae).","authors":"Lei Zhao, Peizhang Chen, Wenchang Li, Zhe Zhang","doi":"10.1080/23802359.2024.2435899","DOIUrl":"10.1080/23802359.2024.2435899","url":null,"abstract":"<p><p>In this study, we report the chloroplast (cp) genome of <i>Dendrobium hainanense</i>. The cp genome was 151,367 bp in length; the overall CG content of the genome was 37.46%. The length of the large single-copy (LSC) region was 83,938 bp, and 15,829 bp in a small single-copy (SSC) region, and a pair of inverted repeats (IRs) of 12,900 bp. One hundred and twenty-seven genes were predicted, including 81 protein-coding genes, 38 genes for tRNA, and eight genes for rRNA. The results of phylogenetic tree showed that <i>Dendrobium hainanense</i> had the closest genetic relationship with <i>Dendrobium parciflorum</i>. This study will be help to understand the genetic diversity of <i>Dendrobium</i>.</p>","PeriodicalId":18647,"journal":{"name":"Mitochondrial DNA. Part B, Resources","volume":"9 12","pages":"1679-1682"},"PeriodicalIF":0.5,"publicationDate":"2024-12-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11633420/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142813859","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"The mitogenomes of two species of sea pigs, <i>Scotoplanes clarki</i> and <i>Protelpidia murrayi</i> (Elasipodida: Holothuroidea: Echinodermata).","authors":"Camryn N Morey, Greg W Rouse","doi":"10.1080/23802359.2024.2438272","DOIUrl":"10.1080/23802359.2024.2438272","url":null,"abstract":"<p><p>Mitochondrial genomes of <i>Scotoplanes</i> <i>clarki</i> and <i>Protelpidia murrayi</i> are presented, each with 13 protein coding genes, two rRNA genes, and 22 tRNA genes. That of <i>Scotoplanes clarki</i> has 15,909 base pairs and that of <i>Protelpidia murrayi</i> is 15,896 base pairs. There is a suspected tandem repeat region of undetermined length in the assemblies of both <i>Scotoplanes clarki</i> and <i>Protelpidia murrayi</i>. The gene order of both mitogenomes is identical to that of other Elasipodida. Phylogenetic analysis revealed that <i>Protelpidia murrayi</i> lies within the <i>Scotoplanes</i> clade, suggesting that <i>Scotoplanes</i> is paraphyletic. Sequencing of the type species, <i>Scotoplanes globosa</i>, is needed to confirm if <i>Protelpidia murrayi</i> should be renamed as <i>Scotoplanes murrayi</i>.</p>","PeriodicalId":18647,"journal":{"name":"Mitochondrial DNA. Part B, Resources","volume":"9 12","pages":"1664-1668"},"PeriodicalIF":0.5,"publicationDate":"2024-12-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11632918/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142813873","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"The first complete mitochondrial genome of <i>Phellinus pomaceus</i> var. <i>prunastri</i> (Pers.) Pat. 1926 (Hymenochaetales: Hymenochaetaceae) and phylogenetic analysis.","authors":"Wei Gao, Shuyi Chen, Qiang Li","doi":"10.1080/23802359.2024.2438275","DOIUrl":"10.1080/23802359.2024.2438275","url":null,"abstract":"<p><p><i>Phellinus pomaceus</i> var. <i>prunastri</i> (Pers.) Pat. 1926 is a famous medicinal fungus that has attracted considerable interest in biotechnology because of its diverse biologically active ingredients. Here, we provide the full mitochondrial genome sequence of <i>P. pomaceus</i>, which spans 122,850 bp and has a GC content of 26.04%. The genome comprises 15 essential protein-coding genes, 26 distinct ORFs, 24 intronic ORFs, 25 tRNAs, and 2 rRNA genes. Bayesian inference (BI) was employed for phylogenetic analysis, revealing the evolutionary relationships among 17 Basidiomycota fungi. The results strongly supported distinct clades and indicated that <i>P. pomaceus</i> is closely related to <i>Fomitiporia mediterranea</i>.</p>","PeriodicalId":18647,"journal":{"name":"Mitochondrial DNA. Part B, Resources","volume":"9 12","pages":"1674-1678"},"PeriodicalIF":0.5,"publicationDate":"2024-12-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11632937/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142813872","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Complete chloroplast genome sequence of the medicinal plant <i>Oxyceros horridus</i> (Rubiaceae) and phylogenetic analysis.","authors":"Thu Thao Thi Huynh, Minh Trong Quang, Hoang Danh Nguyen","doi":"10.1080/23802359.2024.2438281","DOIUrl":"10.1080/23802359.2024.2438281","url":null,"abstract":"<p><p><i>Oxyceros horridus</i> Lour. 1790, valued for ornamental and medicinal properties, has been extensively utilized in traditional medicinal in Vietnam. This study assembled and characterized the first chloroplast of <i>Oxyceros</i> <i>horridus,</i> consisted of 155,333 bp with a GC content of 37.5%. The genome included 130 annotated genes (including 85 protein-coding genes, 37 tRNA genes, and 8 rRNA genes), exhibited a typical quadripartite structure consistent with those found in other members of the Rubiaceae family. Phylogenetic analysis placed <i>O. horridus</i> in Ixoroideae subfamily, closely related to <i>Fosergia shweliensis</i> and <i>Gardenia tenophylla</i>. This study enriches cp genome data and phylogenetic insights within Rubiaceae.</p>","PeriodicalId":18647,"journal":{"name":"Mitochondrial DNA. Part B, Resources","volume":"9 12","pages":"1658-1663"},"PeriodicalIF":0.5,"publicationDate":"2024-12-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11632944/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142813860","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"The complete mitochondrial genome of <i>Proedromys bedfordi</i> Thomas 1911 (Arvicolinae, Rodentia).","authors":"Shiqing Wang, Chen Lin, Zhen Wang, Zhangwen Deng","doi":"10.1080/23802359.2024.2422978","DOIUrl":"10.1080/23802359.2024.2422978","url":null,"abstract":"<p><p>The Duke of Bedford's vole (<i>Proedromys bedfordi</i> Thomas 1911) is distributed only at the border areas of the Sichuan and Gansu Provinces, China. In this study, the first complete mitochondrial genome of <i>P. bedfordi</i> is generated and characterized. The assembled genome is 16,262 base pairs in length and the base compositions present clearly the A-T bias (60.84%). Its genetic constitution and arrangement are consistent with the taxon of the voles, including 13 protein-coding genes, 22 tRNA genes, 2 rRNA genes, and 2 main non-coding regions, D-loop region and O_L region. This mitochondrial genome will be a significant supplement for the genus <i>Proedromys</i> and whole mitogenome phylogenetic analysis provided insights into further evolutionary research of the subfamily Arvicolinae.</p>","PeriodicalId":18647,"journal":{"name":"Mitochondrial DNA. Part B, Resources","volume":"9 12","pages":"1653-1657"},"PeriodicalIF":0.5,"publicationDate":"2024-12-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11632922/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142813871","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"The complete chloroplast genome and phylogenetic analysis of <i>Rubus sumatranus</i> Miq 1861 (Roseaceae).","authors":"Wei Guo, Longyuan Wang, Wei Wu","doi":"10.1080/23802359.2024.2438277","DOIUrl":"10.1080/23802359.2024.2438277","url":null,"abstract":"<p><p>The wild raspberry species <i>Rubus sumatranus</i> Miq 1861 is a promising resource for breeding thermotolerant cultivars. Its complete chloroplast genome spans 155,935 base pairs (bp), featuring the classic quadripartite structure: an 18,729 bp small single-copy region, an 85,662 bp large single-copy region, and two 25,772 bp inverted repeats. A total of 130 genes were identified, including 86 protein-coding, 36 tRNA genes, and 8 rRNA genes. A maximum likelihood phylogenetic tree based on chloroplast genomes shows that <i>R. sumatranus</i>, within the subgenus <i>Idaeobatus</i>, is sister to the subgenus <i>Batothamnus</i>. This confirms the polyphyletic nature of the subgenus <i>Idaeobatus</i>. The chloroplast genome assembly of <i>R. sumatranus</i> enhances our understanding of its evolutionary history.</p>","PeriodicalId":18647,"journal":{"name":"Mitochondrial DNA. Part B, Resources","volume":"9 12","pages":"1669-1673"},"PeriodicalIF":0.5,"publicationDate":"2024-12-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11626868/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142801520","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"The complete mitochondrial genome of <i>Dendrodoris krusensternii</i> (Gastropoda, Nudibranchia, Dendrodorididae) from South Korea.","authors":"Seunghyun Lee, Seongjun Bae","doi":"10.1080/23802359.2024.2435915","DOIUrl":"10.1080/23802359.2024.2435915","url":null,"abstract":"<p><p>The complete mitochondrial genome sequence of <i>Dendrodoris krusensternii</i> (J. E. Gray, 1850) was determined using next-generation sequencing. The complete mitochondrial genome of <i>D. krusensternii</i> is 14,361 bp long, comprising 13 genes, including 13 protein-coding genes (PCGs), 22 transfer RNAs, and two ribosomal RNAs. The nucleotide composition was estimated: 28.7% A, 14.8% C, 19.6% G, and 36.9% T. Phylogenetic analysis was performed using the maximum likelihood method (including 13 PCGs). <i>D. krusensternii</i> is related to the Phyllidiidae (superfamily Phyllidioidea), suggesting a distinct phylogenetic placement within Nudibranchia. This study represents a genomic resource, contributing to molecular studies on the evolution of the Dendrodorididae.</p>","PeriodicalId":18647,"journal":{"name":"Mitochondrial DNA. Part B, Resources","volume":"9 12","pages":"1636-1641"},"PeriodicalIF":0.5,"publicationDate":"2024-12-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11622375/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142801523","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}