比较基因组学和信息含量分析揭示了假单胞菌属中具有基因组水平分辨率的MLSA的核心基因rpoD、pepN和gltX的内部区域

IF 3.6 1区 生物学 Q2 BIOCHEMISTRY & MOLECULAR BIOLOGY
Matías Garavaglia , Andrés Muzlera , Claudio Valverde
{"title":"比较基因组学和信息含量分析揭示了假单胞菌属中具有基因组水平分辨率的MLSA的核心基因rpoD、pepN和gltX的内部区域","authors":"Matías Garavaglia ,&nbsp;Andrés Muzlera ,&nbsp;Claudio Valverde","doi":"10.1016/j.ympev.2022.107663","DOIUrl":null,"url":null,"abstract":"<div><p>In the field of prokaryotic taxonomy, there has been a recent transition towards phylogenomics as the gold standard approach. However, genome-based phylogenetics is still restrictive for its cost when managing large amounts of isolates. Fast, cheap, and taxonomically competent alternatives, like multilocus sequence analysis (MLSA) are thus recommendable. Nevertheless, the criteria for selecting the conserved genes for MLSA have not been explicit for different bacterial taxa, including the broadly diverse <em>Pseudomonas</em> genus. Here, we have carried out an unbiased and rational workflow to select internal sequence regions of <em>Pseudomonas</em> core genes (CG) for a MLSA with the best phylogenetic power, and with a resolution comparable to the genome-based ANI approach. A computational workflow was established to inspect 126 complete genomes of representatives from over 60 <em>Pseudomonas</em> species and subspecies, in order to identify the most informative CG internal regions and determine which combinations in sets of three partial CG sequences have comparable phylogenetic resolution to that of the current ANI standard. We found that the <em>rpoD</em><sup>346-1196</sup>-<em>pepN</em><sup>1711-2571</sup>-<em>gltX</em><sup>86-909</sup> concatenated sequences were the best performing in terms of phylogenetic robustness and resulted highly sensitive and specific when contrasted with ANI. The <em>rpoD</em>-<em>pepN</em>-<em>gltX</em> MLSA was validated <em>in silico</em> and <em>in vitro</em>. Altogether, the results presented here supports the proposal of the <em>rpoD</em>-<em>pepN</em>-<em>gltX</em> MLSA as a fast, affordable, and robust phylogenetic tool for members of the <em>Pseudomonas</em> genus.</p></div>","PeriodicalId":56109,"journal":{"name":"Molecular Phylogenetics and Evolution","volume":"179 ","pages":"Article 107663"},"PeriodicalIF":3.6000,"publicationDate":"2023-02-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":"1","resultStr":"{\"title\":\"Comparative genomics and informational content analysis uncovered internal regions of the core genes rpoD, pepN and gltX for an MLSA with genome-level resolving power within the genus Pseudomonas\",\"authors\":\"Matías Garavaglia ,&nbsp;Andrés Muzlera ,&nbsp;Claudio Valverde\",\"doi\":\"10.1016/j.ympev.2022.107663\",\"DOIUrl\":null,\"url\":null,\"abstract\":\"<div><p>In the field of prokaryotic taxonomy, there has been a recent transition towards phylogenomics as the gold standard approach. However, genome-based phylogenetics is still restrictive for its cost when managing large amounts of isolates. Fast, cheap, and taxonomically competent alternatives, like multilocus sequence analysis (MLSA) are thus recommendable. Nevertheless, the criteria for selecting the conserved genes for MLSA have not been explicit for different bacterial taxa, including the broadly diverse <em>Pseudomonas</em> genus. Here, we have carried out an unbiased and rational workflow to select internal sequence regions of <em>Pseudomonas</em> core genes (CG) for a MLSA with the best phylogenetic power, and with a resolution comparable to the genome-based ANI approach. A computational workflow was established to inspect 126 complete genomes of representatives from over 60 <em>Pseudomonas</em> species and subspecies, in order to identify the most informative CG internal regions and determine which combinations in sets of three partial CG sequences have comparable phylogenetic resolution to that of the current ANI standard. We found that the <em>rpoD</em><sup>346-1196</sup>-<em>pepN</em><sup>1711-2571</sup>-<em>gltX</em><sup>86-909</sup> concatenated sequences were the best performing in terms of phylogenetic robustness and resulted highly sensitive and specific when contrasted with ANI. The <em>rpoD</em>-<em>pepN</em>-<em>gltX</em> MLSA was validated <em>in silico</em> and <em>in vitro</em>. Altogether, the results presented here supports the proposal of the <em>rpoD</em>-<em>pepN</em>-<em>gltX</em> MLSA as a fast, affordable, and robust phylogenetic tool for members of the <em>Pseudomonas</em> genus.</p></div>\",\"PeriodicalId\":56109,\"journal\":{\"name\":\"Molecular Phylogenetics and Evolution\",\"volume\":\"179 \",\"pages\":\"Article 107663\"},\"PeriodicalIF\":3.6000,\"publicationDate\":\"2023-02-01\",\"publicationTypes\":\"Journal Article\",\"fieldsOfStudy\":null,\"isOpenAccess\":false,\"openAccessPdf\":\"\",\"citationCount\":\"1\",\"resultStr\":null,\"platform\":\"Semanticscholar\",\"paperid\":null,\"PeriodicalName\":\"Molecular Phylogenetics and Evolution\",\"FirstCategoryId\":\"99\",\"ListUrlMain\":\"https://www.sciencedirect.com/science/article/pii/S1055790322002767\",\"RegionNum\":1,\"RegionCategory\":\"生物学\",\"ArticlePicture\":[],\"TitleCN\":null,\"AbstractTextCN\":null,\"PMCID\":null,\"EPubDate\":\"\",\"PubModel\":\"\",\"JCR\":\"Q2\",\"JCRName\":\"BIOCHEMISTRY & MOLECULAR BIOLOGY\",\"Score\":null,\"Total\":0}","platform":"Semanticscholar","paperid":null,"PeriodicalName":"Molecular Phylogenetics and Evolution","FirstCategoryId":"99","ListUrlMain":"https://www.sciencedirect.com/science/article/pii/S1055790322002767","RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":null,"EPubDate":"","PubModel":"","JCR":"Q2","JCRName":"BIOCHEMISTRY & MOLECULAR BIOLOGY","Score":null,"Total":0}
引用次数: 1

摘要

在原核分类学领域,最近有一个向系统发育组学作为金标准方法的转变。然而,在管理大量分离株时,基于基因组的系统发育学仍然因其成本而受到限制。因此,推荐快速、廉价且具有分类学能力的替代方案,如多焦点序列分析(MLSA)。然而,对于不同的细菌分类群,包括广泛多样的假单胞菌属,选择MLSA保守基因的标准尚未明确。在这里,我们进行了一个公正合理的工作流程,为具有最佳系统发育能力的MLSA选择假单胞菌核心基因(CG)的内部序列区域,其分辨率与基于基因组的ANI方法相当。建立了一个计算工作流程来检查来自60多个假单胞菌物种和亚种的126个代表性完整基因组,以确定信息量最大的CG内部区域,并确定三个部分CG序列中的哪些组合具有与当前ANI标准相当的系统发育分辨率。我们发现rpoD346-1196-epN1711-2571-gltX86-909串联序列在系统发育稳健性方面表现最好,与ANI相比具有高度敏感性和特异性。rpo-pepN-gltX-MLSA在计算机和体外进行了验证。总之,本文的结果支持了rpoD-pepN-gltX-MLSA作为假单胞菌属成员的快速、负担得起和强大的系统发育工具的建议。
本文章由计算机程序翻译,如有差异,请以英文原文为准。

Comparative genomics and informational content analysis uncovered internal regions of the core genes rpoD, pepN and gltX for an MLSA with genome-level resolving power within the genus Pseudomonas

Comparative genomics and informational content analysis uncovered internal regions of the core genes rpoD, pepN and gltX for an MLSA with genome-level resolving power within the genus Pseudomonas

In the field of prokaryotic taxonomy, there has been a recent transition towards phylogenomics as the gold standard approach. However, genome-based phylogenetics is still restrictive for its cost when managing large amounts of isolates. Fast, cheap, and taxonomically competent alternatives, like multilocus sequence analysis (MLSA) are thus recommendable. Nevertheless, the criteria for selecting the conserved genes for MLSA have not been explicit for different bacterial taxa, including the broadly diverse Pseudomonas genus. Here, we have carried out an unbiased and rational workflow to select internal sequence regions of Pseudomonas core genes (CG) for a MLSA with the best phylogenetic power, and with a resolution comparable to the genome-based ANI approach. A computational workflow was established to inspect 126 complete genomes of representatives from over 60 Pseudomonas species and subspecies, in order to identify the most informative CG internal regions and determine which combinations in sets of three partial CG sequences have comparable phylogenetic resolution to that of the current ANI standard. We found that the rpoD346-1196-pepN1711-2571-gltX86-909 concatenated sequences were the best performing in terms of phylogenetic robustness and resulted highly sensitive and specific when contrasted with ANI. The rpoD-pepN-gltX MLSA was validated in silico and in vitro. Altogether, the results presented here supports the proposal of the rpoD-pepN-gltX MLSA as a fast, affordable, and robust phylogenetic tool for members of the Pseudomonas genus.

求助全文
通过发布文献求助,成功后即可免费获取论文全文。 去求助
来源期刊
Molecular Phylogenetics and Evolution
Molecular Phylogenetics and Evolution 生物-进化生物学
CiteScore
7.50
自引率
7.30%
发文量
249
审稿时长
7.5 months
期刊介绍: Molecular Phylogenetics and Evolution is dedicated to bringing Darwin''s dream within grasp - to "have fairly true genealogical trees of each great kingdom of Nature." The journal provides a forum for molecular studies that advance our understanding of phylogeny and evolution, further the development of phylogenetically more accurate taxonomic classifications, and ultimately bring a unified classification for all the ramifying lines of life. Phylogeographic studies will be considered for publication if they offer EXCEPTIONAL theoretical or empirical advances.
×
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:604180095
Book学术官方微信