Comparative genomics revealed new insights into the plastome evolution of Ludwigia (Onagraceae, Myrtales).

IF 2.6 4区 综合性期刊 Q2 MULTIDISCIPLINARY SCIENCES Science Progress Pub Date : 2024-07-01 DOI:10.1177/00368504241272741
Hoang Danh Nguyen, Hoang Dang Khoa Do, Minh Thiet Vu
{"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}
引用次数: 0

Abstract

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.

查看原文
分享 分享
微信好友 朋友圈 QQ好友 复制链接
本刊更多论文
比较基因组学揭示了 Ludwigia(Onagraceae, Myrtales)质体进化的新见解。
报春花柳属(Ludwigia L.)是一种定义明确的大戟科属植物,共有 87 个种,广泛分布于世界各地。在这项研究中,我们对该属的三个物种,包括 Ludwigia adscendens、Ludwigia hyssopifolia 和 Ludwigia prostrata 的完整叶绿体(cp)基因组进行了测序和鉴定。三个Ludwigia cp基因组的大小从158,354到159,592 bp不等,每个基因组包含113个基因,包括79个独特的蛋白质编码基因(PCGs)、4个rRNA基因和30个tRNA基因。对路德维格 cp 基因组进行比较后发现,它们在基因组成、基因方向和 GC 含量方面高度保守。此外,我们还比较了 cp 基因组的结构,并重建了与大戟科相关物种的系统发育关系。在倒位重复区(IR)的收缩/扩张方面,在Oenothera属、Chamaenerion属和Epilobium属中发现了两种扩张的IR区结构,在Ludwigia属和Circeae属中发现了原始的IR区结构。clpP、ycf2和ycf1基因区域在Onagraceae科所有可获得的cp基因组中具有高度差异的核苷酸。利用 39 个 Onagraceae cp 基因组中的 79 个 PCGs 进行系统发育重建,推断 Ludwigia(包括 L. adscendens、L. hyssopifolia、L. prostrata 和 Ludwigia octovalvis)支系为单系,并得到引导值和后验概率值的良好支持。本研究提供了三个Ludwigia物种的参考cp基因组,可用于Ludwigia和Onagraceae类群的物种鉴定和系统发育重建。
本文章由计算机程序翻译,如有差异,请以英文原文为准。
求助全文
约1分钟内获得全文 去求助
来源期刊
Science Progress
Science Progress Multidisciplinary-Multidisciplinary
CiteScore
3.80
自引率
0.00%
发文量
119
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.
期刊最新文献
A voltage mode grounded capacitance multiplier with widely tunable gain for ultra-low cutoff frequency filter. Appropriate dose of tranexamic acid in the topical treatment of anterior epistaxis, 500 mg vs 1000 mg: A double-blind randomized controlled trial. Research status and prospect of flexible optimization design methodology of propeller CNC polishing machines. Sliding mode control with self-adaptive parameters of a 5-DOF hybrid robot. Spoofing attack recognition for GNSS-based train positioning using a BO-LightGBM method.
×
引用
GB/T 7714-2015
复制
MLA
复制
APA
复制
导出至
BibTeX EndNote RefMan NoteFirst NoteExpress
×
×
提示
您的信息不完整,为了账户安全,请先补充。
现在去补充
×
提示
您因"违规操作"
具体请查看互助需知
我知道了
×
提示
现在去查看 取消
×
提示
确定
0
微信
客服QQ
Book学术公众号 扫码关注我们
反馈
×
意见反馈
请填写您的意见或建议
请填写您的手机或邮箱
已复制链接
已复制链接
快去分享给好友吧!
我知道了
×
扫码分享
扫码分享
Book学术官方微信
Book学术文献互助
Book学术文献互助群
群 号:481959085
Book学术
文献互助 智能选刊 最新文献 互助须知 联系我们:info@booksci.cn
Book学术提供免费学术资源搜索服务,方便国内外学者检索中英文文献。致力于提供最便捷和优质的服务体验。
Copyright © 2023 Book学术 All rights reserved.
ghs 京公网安备 11010802042870号 京ICP备2023020795号-1