Phylogenetic analysis of Lamiaceae based on transcriptome data

IF 1.7 4区 生物学 Q4 BIOTECHNOLOGY & APPLIED MICROBIOLOGY
Hyewon Kim, Yuna Kang, Wonkyun Joo, Changsoo Kim
{"title":"Phylogenetic analysis of Lamiaceae based on transcriptome data","authors":"Hyewon Kim, Yuna Kang, Wonkyun Joo, Changsoo Kim","doi":"10.1007/s11816-023-00869-y","DOIUrl":null,"url":null,"abstract":"<p>The Lamiaceae family is included in the angiosperms and comprises over 7000 species, many of which are of considerable ecological, economic, and cultural importance. We seek to establish a taxonomic basis by examining the speciation timeline in Lamiaceae using phylogenetics and publicly available transcriptome data. Since Ks is steadily accumulated over time in plants for environmental adaptation until speciation occurs, the timing of speciation can be estimated from examination of Ks values. A total of 24 species included in the Lamiaceae family used in our analysis belongs to four subfamilies. We performed transcriptome assembly for each of the 24 species using trimmed data collected from public databases. We compiled groups of gene families in which at least one copy of the gene is present in each species from orthologous groups among unigenes. From these groups, we obtained a total of 450,014 single nucleotide polymorphisms (SNPs) across 27 species, incorporating three additional outgroup species. Subsequently, a tree was created using these SNPs. In our tree, the outgroup species were clearly located externally, confirming the proximity of species within the same subfamily. The Ks peak corroborated the outcomes observed in the phylogenetic tree. We estimated the rate of sequence evolution and divergence time for each species on the phylogenetic tree by referencing the time of divergence among the Lamiaceae family. In particular, <i>Clinopodium serpyllifolium</i>, <i>Lavandula</i> × <i>intermedia</i>, <i>Phlomis fruticosa</i>, and <i>Volkameria inermis</i> were analyzed for the first time. Our study helps with the understanding of the function of plants included in the Lamiaceae family and is expected to provide a fundamental resource that can be used to pinpoint the molecular and genomic evolution of the Lamiaceae family.</p>","PeriodicalId":20216,"journal":{"name":"Plant Biotechnology Reports","volume":null,"pages":null},"PeriodicalIF":1.7000,"publicationDate":"2023-11-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":"0","resultStr":null,"platform":"Semanticscholar","paperid":null,"PeriodicalName":"Plant Biotechnology Reports","FirstCategoryId":"5","ListUrlMain":"https://doi.org/10.1007/s11816-023-00869-y","RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":null,"EPubDate":"","PubModel":"","JCR":"Q4","JCRName":"BIOTECHNOLOGY & APPLIED MICROBIOLOGY","Score":null,"Total":0}
引用次数: 0

Abstract

The Lamiaceae family is included in the angiosperms and comprises over 7000 species, many of which are of considerable ecological, economic, and cultural importance. We seek to establish a taxonomic basis by examining the speciation timeline in Lamiaceae using phylogenetics and publicly available transcriptome data. Since Ks is steadily accumulated over time in plants for environmental adaptation until speciation occurs, the timing of speciation can be estimated from examination of Ks values. A total of 24 species included in the Lamiaceae family used in our analysis belongs to four subfamilies. We performed transcriptome assembly for each of the 24 species using trimmed data collected from public databases. We compiled groups of gene families in which at least one copy of the gene is present in each species from orthologous groups among unigenes. From these groups, we obtained a total of 450,014 single nucleotide polymorphisms (SNPs) across 27 species, incorporating three additional outgroup species. Subsequently, a tree was created using these SNPs. In our tree, the outgroup species were clearly located externally, confirming the proximity of species within the same subfamily. The Ks peak corroborated the outcomes observed in the phylogenetic tree. We estimated the rate of sequence evolution and divergence time for each species on the phylogenetic tree by referencing the time of divergence among the Lamiaceae family. In particular, Clinopodium serpyllifolium, Lavandula × intermedia, Phlomis fruticosa, and Volkameria inermis were analyzed for the first time. Our study helps with the understanding of the function of plants included in the Lamiaceae family and is expected to provide a fundamental resource that can be used to pinpoint the molecular and genomic evolution of the Lamiaceae family.

Abstract Image

基于转录组数据的紫唇科植物系统发育分析
叶面科是被子植物的一种,有7000多种,其中许多具有重要的生态、经济和文化意义。我们试图通过使用系统发育学和公开可用的转录组数据来检查Lamiaceae的物种形成时间表,从而建立分类基础。由于Ks在植物中随着时间的推移稳定地积累以适应环境,直到物种形成,因此可以通过检查Ks值来估计物种形成的时间。我们所使用的Lamiaceae科共24种,分属4个亚科。我们使用从公共数据库收集的修剪数据对24个物种中的每个物种进行转录组组装。我们编译了一组基因家族,其中至少有一个拷贝的基因存在于每个物种的同源群之间的单基因。从这些群体中,我们获得了27个物种的450,014个单核苷酸多态性(SNPs),包括三个额外的外群物种。随后,利用这些snp创建了一个树。在我们的树中,外群物种明显位于外部,证实了同一亚科内物种的接近性。Ks峰证实了在系统发育树上观察到的结果。我们参考了Lamiaceae科的分化时间,估计了系统发育树上各物种的序列进化速率和分化时间。其中,丝绵草(Clinopodium serpyllifolium)、中间薰衣草(Lavandula x intermedia)、紫茎草(Phlomis fruticosa)和藜草(Volkameria inermis)首次被分析。我们的研究有助于了解Lamiaceae家族植物的功能,并有望为Lamiaceae家族的分子和基因组进化提供基础资源。
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 求助全文
来源期刊
Plant Biotechnology Reports
Plant Biotechnology Reports 生物-生物工程与应用微生物
CiteScore
4.10
自引率
4.20%
发文量
72
审稿时长
>12 weeks
期刊介绍: Plant Biotechnology Reports publishes original, peer-reviewed articles dealing with all aspects of fundamental and applied research in the field of plant biotechnology, which includes molecular biology, genetics, biochemistry, cell and tissue culture, production of secondary metabolites, metabolic engineering, genomics, proteomics, and metabolomics. Plant Biotechnology Reports emphasizes studies on plants indigenous to the Asia-Pacific region and studies related to commercialization of plant biotechnology. Plant Biotechnology Reports does not exclude studies on lower plants including algae and cyanobacteria if studies are carried out within the aspects described above.
×
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
确定
请完成安全验证×
copy
已复制链接
快去分享给好友吧!
我知道了
右上角分享
点击右上角分享
0
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 布克学术 All rights reserved.
京ICP备2023020795号-1
ghs 京公网安备 11010802042870号
Book学术文献互助
Book学术文献互助群
群 号:481959085
Book学术官方微信