Guang-Hua Liu , You-Wei Zuo , Yuanyu Shan , Jie Yu , Jia-Xi Li , Ying Chen , Xin-Yi Gong , Xiao-Min Liao
{"title":"对檀香树线粒体基因组的结构分析显示出复杂的分支结构。","authors":"Guang-Hua Liu , You-Wei Zuo , Yuanyu Shan , Jie Yu , Jia-Xi Li , Ying Chen , Xin-Yi Gong , Xiao-Min Liao","doi":"10.1016/j.ygeno.2024.110935","DOIUrl":null,"url":null,"abstract":"<div><h3>Background</h3><p><em>Santalum album</em> L. is an evergreen tree which is mainly distributes throughout tropical and temperate regions. And it has a great medicinal and economic value.</p></div><div><h3>Results</h3><p>In this study, the complete mitochondrial genome of <em>S. album</em> were assembled and annotated, which could be descried by a complex branched structure consisting of three contigs. The lengths of these three contigs are 165,122 bp, 93,430 bp and 92,491 bp. We annotated 34 genes coding for proteins (PCGs), 26 tRNA genes, and 4 rRNA genes. The analysis of repeated elements shows that there are 89 SSRs and 242 pairs of dispersed repeats in <em>S. album</em> mitochondrial genome. Also we found 20 MTPTs among the chloroplast and mitochondria. The 20 MTPTs sequences span a combined length of 22,353 bp, making up 15.52 % of the plastome, 6.37 % of the mitochondrial genome. Additionally, by using the Deepred-mt tool, we found 628 RNA editing sites in 34 PCGs. Moreover, significant genomic rearrangement is observed between <em>S. album</em> and its associated mitochondrial genomes. Finally, based on mitochondrial genome PCGs, we deduced the phylogenetic ties between <em>S. album</em> and other angiosperms.</p></div><div><h3>Conclusions</h3><p>We reported the mitochondrial genome from Santalales for the first time, which provides a crucial genetic resource for our study of the evolution of mitochondrial genome.</p></div>","PeriodicalId":12521,"journal":{"name":"Genomics","volume":"116 5","pages":"Article 110935"},"PeriodicalIF":3.4000,"publicationDate":"2024-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.sciencedirect.com/science/article/pii/S0888754324001563/pdfft?md5=f8c9aae391b32e116113b9fb2e29933f&pid=1-s2.0-S0888754324001563-main.pdf","citationCount":"0","resultStr":"{\"title\":\"Structural analysis of the mitochondrial genome of Santalum album reveals a complex branched configuration\",\"authors\":\"Guang-Hua Liu , You-Wei Zuo , Yuanyu Shan , Jie Yu , Jia-Xi Li , Ying Chen , Xin-Yi Gong , Xiao-Min Liao\",\"doi\":\"10.1016/j.ygeno.2024.110935\",\"DOIUrl\":null,\"url\":null,\"abstract\":\"<div><h3>Background</h3><p><em>Santalum album</em> L. is an evergreen tree which is mainly distributes throughout tropical and temperate regions. And it has a great medicinal and economic value.</p></div><div><h3>Results</h3><p>In this study, the complete mitochondrial genome of <em>S. album</em> were assembled and annotated, which could be descried by a complex branched structure consisting of three contigs. The lengths of these three contigs are 165,122 bp, 93,430 bp and 92,491 bp. We annotated 34 genes coding for proteins (PCGs), 26 tRNA genes, and 4 rRNA genes. The analysis of repeated elements shows that there are 89 SSRs and 242 pairs of dispersed repeats in <em>S. album</em> mitochondrial genome. Also we found 20 MTPTs among the chloroplast and mitochondria. The 20 MTPTs sequences span a combined length of 22,353 bp, making up 15.52 % of the plastome, 6.37 % of the mitochondrial genome. Additionally, by using the Deepred-mt tool, we found 628 RNA editing sites in 34 PCGs. Moreover, significant genomic rearrangement is observed between <em>S. album</em> and its associated mitochondrial genomes. Finally, based on mitochondrial genome PCGs, we deduced the phylogenetic ties between <em>S. album</em> and other angiosperms.</p></div><div><h3>Conclusions</h3><p>We reported the mitochondrial genome from Santalales for the first time, which provides a crucial genetic resource for our study of the evolution of mitochondrial genome.</p></div>\",\"PeriodicalId\":12521,\"journal\":{\"name\":\"Genomics\",\"volume\":\"116 5\",\"pages\":\"Article 110935\"},\"PeriodicalIF\":3.4000,\"publicationDate\":\"2024-09-01\",\"publicationTypes\":\"Journal Article\",\"fieldsOfStudy\":null,\"isOpenAccess\":false,\"openAccessPdf\":\"https://www.sciencedirect.com/science/article/pii/S0888754324001563/pdfft?md5=f8c9aae391b32e116113b9fb2e29933f&pid=1-s2.0-S0888754324001563-main.pdf\",\"citationCount\":\"0\",\"resultStr\":null,\"platform\":\"Semanticscholar\",\"paperid\":null,\"PeriodicalName\":\"Genomics\",\"FirstCategoryId\":\"99\",\"ListUrlMain\":\"https://www.sciencedirect.com/science/article/pii/S0888754324001563\",\"RegionNum\":2,\"RegionCategory\":\"生物学\",\"ArticlePicture\":[],\"TitleCN\":null,\"AbstractTextCN\":null,\"PMCID\":null,\"EPubDate\":\"\",\"PubModel\":\"\",\"JCR\":\"Q2\",\"JCRName\":\"BIOTECHNOLOGY & APPLIED MICROBIOLOGY\",\"Score\":null,\"Total\":0}","platform":"Semanticscholar","paperid":null,"PeriodicalName":"Genomics","FirstCategoryId":"99","ListUrlMain":"https://www.sciencedirect.com/science/article/pii/S0888754324001563","RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":null,"EPubDate":"","PubModel":"","JCR":"Q2","JCRName":"BIOTECHNOLOGY & APPLIED MICROBIOLOGY","Score":null,"Total":0}
引用次数: 0
摘要
背景介绍枋属常绿乔木，主要分布于热带和温带地区。其药用和经济价值极高：本研究组装并注释了檀香树的完整线粒体基因组。这三个等位基因的长度分别为 165,122 bp、93,430 bp 和 92,491 bp。我们注释了 34 个编码蛋白质的基因（PCGs）、26 个 tRNA 基因和 4 个 rRNA 基因。重复序列分析表明，S. album 线粒体基因组中有 89 个 SSR 和 242 对分散重复序列。此外，我们还在叶绿体和线粒体中发现了 20 个 MTPTs。这 20 个 MTPTs 序列的总长度为 22,353 bp，占质体基因组的 15.52%，线粒体基因组的 6.37%。此外，通过使用 Deepred-mt 工具，我们在 34 个 PCGs 中发现了 628 个 RNA 编辑位点。此外，在 S. album 及其相关线粒体基因组之间还发现了明显的基因组重排现象。最后，根据线粒体基因组 PCGs，我们推断出了白相思与其他被子植物之间的系统发育关系：我们首次报道了山桐子的线粒体基因组，这为我们研究线粒体基因组的进化提供了重要的遗传资源。
Structural analysis of the mitochondrial genome of Santalum album reveals a complex branched configuration
Background
Santalum album L. is an evergreen tree which is mainly distributes throughout tropical and temperate regions. And it has a great medicinal and economic value.
Results
In this study, the complete mitochondrial genome of S. album were assembled and annotated, which could be descried by a complex branched structure consisting of three contigs. The lengths of these three contigs are 165,122 bp, 93,430 bp and 92,491 bp. We annotated 34 genes coding for proteins (PCGs), 26 tRNA genes, and 4 rRNA genes. The analysis of repeated elements shows that there are 89 SSRs and 242 pairs of dispersed repeats in S. album mitochondrial genome. Also we found 20 MTPTs among the chloroplast and mitochondria. The 20 MTPTs sequences span a combined length of 22,353 bp, making up 15.52 % of the plastome, 6.37 % of the mitochondrial genome. Additionally, by using the Deepred-mt tool, we found 628 RNA editing sites in 34 PCGs. Moreover, significant genomic rearrangement is observed between S. album and its associated mitochondrial genomes. Finally, based on mitochondrial genome PCGs, we deduced the phylogenetic ties between S. album and other angiosperms.
Conclusions
We reported the mitochondrial genome from Santalales for the first time, which provides a crucial genetic resource for our study of the evolution of mitochondrial genome.
期刊介绍：
Genomics is a forum for describing the development of genome-scale technologies and their application to all areas of biological investigation.
As a journal that has evolved with the field that carries its name, Genomics focuses on the development and application of cutting-edge methods, addressing fundamental questions with potential interest to a wide audience. Our aim is to publish the highest quality research and to provide authors with rapid, fair and accurate review and publication of manuscripts falling within our scope.
求助内容：
应助结果提醒方式：
京公网安备 11010802042870号
