Hoang Danh Nguyen, Hoang Dang Khoa Do, Minh Thiet Vu
{"title":"比较基因组学揭示了 Ludwigia(Onagraceae, Myrtales)质体进化的新见解。","authors":"Hoang Danh Nguyen, Hoang Dang Khoa Do, Minh Thiet Vu","doi":"10.1177/00368504241272741","DOIUrl":null,"url":null,"abstract":"<p><p>The primrose-willow (<i>Ludwigia</i> L.), a well-defined genus of the Onagraceae family, comprises 87 species widely distributed worldwide. In this study, we sequenced and characterized the complete chloroplast (cp) genomes of three species in the genus, including <i>Ludwigia adscendens</i>, <i>Ludwigia hyssopifolia</i>, and <i>Ludwigia prostrata</i>. Three <i>Ludwigia</i> cp genomes ranged from 158,354 to 159,592 bp in size, and each contained 113 genes, including 79 unique protein-coding genes (PCGs), four rRNA genes, and 30 tRNA genes. A comparison of the <i>Ludwigia</i> cp genomes revealed that they were highly conserved in gene composition, gene orientation, and GC content. Moreover, we compared the structure of cp genomes and reconstructed phylogenetic relationships with related species in the Onagraceae family. Regarding contraction/expansion of inverted repeat (IR) region, two kinds of expansion IR region structures were found in <i>Oenothera</i>, <i>Chamaenerion</i>, and <i>Epilobium</i> genera, with primitive IR structures in <i>Ludwigia</i> and <i>Circeae</i> genera. The regions <i>clpP</i>, <i>ycf2</i>, and <i>ycf1</i> genes possessed highly divergent nucleotides among all available cp genomes of the Onagraceae family. The phylogenetic reconstruction using 79 PCGs from 39 Onagraceae cp genomes inferred that <i>Ludwigia</i> (including <i>L. adscendens</i>, <i>L. hyssopifolia</i>, <i>L. prostrata</i>, and <i>Ludwigia octovalvis</i>) clade was monophyletic and well-supported by the bootstrap and posterior probability values. This study provides the reference cp genomes of three <i>Ludwigia</i> species, which can be used for species identification and phylogenetic reconstruction of <i>Ludwigia</i> and Onagraceae taxa.</p>","PeriodicalId":56061,"journal":{"name":"Science Progress","volume":null,"pages":null},"PeriodicalIF":2.6000,"publicationDate":"2024-07-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11329976/pdf/","citationCount":"0","resultStr":"{\"title\":\"Comparative genomics revealed new insights into the plastome evolution of <i>Ludwigia</i> (Onagraceae, Myrtales).\",\"authors\":\"Hoang Danh Nguyen, Hoang Dang Khoa Do, Minh Thiet Vu\",\"doi\":\"10.1177/00368504241272741\",\"DOIUrl\":null,\"url\":null,\"abstract\":\"<p><p>The primrose-willow (<i>Ludwigia</i> L.), a well-defined genus of the Onagraceae family, comprises 87 species widely distributed worldwide. In this study, we sequenced and characterized the complete chloroplast (cp) genomes of three species in the genus, including <i>Ludwigia adscendens</i>, <i>Ludwigia hyssopifolia</i>, and <i>Ludwigia prostrata</i>. Three <i>Ludwigia</i> cp genomes ranged from 158,354 to 159,592 bp in size, and each contained 113 genes, including 79 unique protein-coding genes (PCGs), four rRNA genes, and 30 tRNA genes. A comparison of the <i>Ludwigia</i> cp genomes revealed that they were highly conserved in gene composition, gene orientation, and GC content. Moreover, we compared the structure of cp genomes and reconstructed phylogenetic relationships with related species in the Onagraceae family. Regarding contraction/expansion of inverted repeat (IR) region, two kinds of expansion IR region structures were found in <i>Oenothera</i>, <i>Chamaenerion</i>, and <i>Epilobium</i> genera, with primitive IR structures in <i>Ludwigia</i> and <i>Circeae</i> genera. The regions <i>clpP</i>, <i>ycf2</i>, and <i>ycf1</i> genes possessed highly divergent nucleotides among all available cp genomes of the Onagraceae family. The phylogenetic reconstruction using 79 PCGs from 39 Onagraceae cp genomes inferred that <i>Ludwigia</i> (including <i>L. adscendens</i>, <i>L. hyssopifolia</i>, <i>L. prostrata</i>, and <i>Ludwigia octovalvis</i>) clade was monophyletic and well-supported by the bootstrap and posterior probability values. This study provides the reference cp genomes of three <i>Ludwigia</i> species, which can be used for species identification and phylogenetic reconstruction of <i>Ludwigia</i> and Onagraceae taxa.</p>\",\"PeriodicalId\":56061,\"journal\":{\"name\":\"Science Progress\",\"volume\":null,\"pages\":null},\"PeriodicalIF\":2.6000,\"publicationDate\":\"2024-07-01\",\"publicationTypes\":\"Journal Article\",\"fieldsOfStudy\":null,\"isOpenAccess\":false,\"openAccessPdf\":\"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11329976/pdf/\",\"citationCount\":\"0\",\"resultStr\":null,\"platform\":\"Semanticscholar\",\"paperid\":null,\"PeriodicalName\":\"Science Progress\",\"FirstCategoryId\":\"103\",\"ListUrlMain\":\"https://doi.org/10.1177/00368504241272741\",\"RegionNum\":4,\"RegionCategory\":\"综合性期刊\",\"ArticlePicture\":[],\"TitleCN\":null,\"AbstractTextCN\":null,\"PMCID\":null,\"EPubDate\":\"\",\"PubModel\":\"\",\"JCR\":\"Q2\",\"JCRName\":\"MULTIDISCIPLINARY SCIENCES\",\"Score\":null,\"Total\":0}","platform":"Semanticscholar","paperid":null,"PeriodicalName":"Science Progress","FirstCategoryId":"103","ListUrlMain":"https://doi.org/10.1177/00368504241272741","RegionNum":4,"RegionCategory":"综合性期刊","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":null,"EPubDate":"","PubModel":"","JCR":"Q2","JCRName":"MULTIDISCIPLINARY SCIENCES","Score":null,"Total":0}
Comparative genomics revealed new insights into the plastome evolution of Ludwigia (Onagraceae, Myrtales).
The primrose-willow (Ludwigia L.), a well-defined genus of the Onagraceae family, comprises 87 species widely distributed worldwide. In this study, we sequenced and characterized the complete chloroplast (cp) genomes of three species in the genus, including Ludwigia adscendens, Ludwigia hyssopifolia, and Ludwigia prostrata. Three Ludwigia cp genomes ranged from 158,354 to 159,592 bp in size, and each contained 113 genes, including 79 unique protein-coding genes (PCGs), four rRNA genes, and 30 tRNA genes. A comparison of the Ludwigia cp genomes revealed that they were highly conserved in gene composition, gene orientation, and GC content. Moreover, we compared the structure of cp genomes and reconstructed phylogenetic relationships with related species in the Onagraceae family. Regarding contraction/expansion of inverted repeat (IR) region, two kinds of expansion IR region structures were found in Oenothera, Chamaenerion, and Epilobium genera, with primitive IR structures in Ludwigia and Circeae genera. The regions clpP, ycf2, and ycf1 genes possessed highly divergent nucleotides among all available cp genomes of the Onagraceae family. The phylogenetic reconstruction using 79 PCGs from 39 Onagraceae cp genomes inferred that Ludwigia (including L. adscendens, L. hyssopifolia, L. prostrata, and Ludwigia octovalvis) clade was monophyletic and well-supported by the bootstrap and posterior probability values. This study provides the reference cp genomes of three Ludwigia species, which can be used for species identification and phylogenetic reconstruction of Ludwigia and Onagraceae taxa.
期刊介绍:
Science Progress has for over 100 years been a highly regarded review publication in science, technology and medicine. Its objective is to excite the readers'' interest in areas with which they may not be fully familiar but which could facilitate their interest, or even activity, in a cognate field.