Henry D. Naranjo , Liesbeth Lebbe , Margo Cnockaert , Florent Lassalle , Chin Chin Too , Anne Willems
{"title":"Phylogenomics reveals insights into the functional evolution of the genus Agrobacterium and enables the description of Agrobacterium divergens sp. nov","authors":"Henry D. Naranjo , Liesbeth Lebbe , Margo Cnockaert , Florent Lassalle , Chin Chin Too , Anne Willems","doi":"10.1016/j.syapm.2023.126420","DOIUrl":null,"url":null,"abstract":"<div><p>The genus <span><em>Agrobacterium</em></span> was initially described as mainly phytopathogenic strains. Nowadays, the genus includes phytopathogenic and non-phytopathogenic bacteria that are distinctive among the <span><em>Rhizobiaceae</em></span> family. Recently we have isolated two closely related strains, LMG 31531<sup>T</sup> and LMG 31532, from soil and plant roots, respectively. Both strains differ from previously reported species based on the genomic and phenotypic data. <em>A. arsenijevicii</em> KFB 330<sup>T</sup> and <em>A. fabacearum</em> LMG 31642<sup>T</sup> showed the highest 16S rRNA similarity (98.9 %), followed by <em>A. nepotum</em> LMG 26435<sup>T</sup> (98.7 %). A clear genomic feature that distinguishes LMG 31531<sup>T</sup> and LMG 31532 from other <em>Agrobacterium</em><span> species is the absence of a linear chromid. Nevertheless, typical values of the core-proteome Average Amino Acid Identity (cpAAI > 85 %) and 16S rRNA gene sequence similarity (>96 %) when compared to other members of the genus confirm the position of these two strains as part of the </span><em>Agrobacterium</em> genus. They are therefore described as <em>Agrobacterium divergens</em> sp. nov. Besides, our comparative genomic study and survey for clade-specific markers resulted in the discovery of conserved proteins that provide insights into the functional evolution of this genus.</p></div>","PeriodicalId":22124,"journal":{"name":"Systematic and applied microbiology","volume":"46 3","pages":"Article 126420"},"PeriodicalIF":3.3000,"publicationDate":"2023-05-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":"1","resultStr":null,"platform":"Semanticscholar","paperid":null,"PeriodicalName":"Systematic and applied microbiology","FirstCategoryId":"99","ListUrlMain":"https://www.sciencedirect.com/science/article/pii/S0723202023000292","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: 1
Abstract
The genus Agrobacterium was initially described as mainly phytopathogenic strains. Nowadays, the genus includes phytopathogenic and non-phytopathogenic bacteria that are distinctive among the Rhizobiaceae family. Recently we have isolated two closely related strains, LMG 31531T and LMG 31532, from soil and plant roots, respectively. Both strains differ from previously reported species based on the genomic and phenotypic data. A. arsenijevicii KFB 330T and A. fabacearum LMG 31642T showed the highest 16S rRNA similarity (98.9 %), followed by A. nepotum LMG 26435T (98.7 %). A clear genomic feature that distinguishes LMG 31531T and LMG 31532 from other Agrobacterium species is the absence of a linear chromid. Nevertheless, typical values of the core-proteome Average Amino Acid Identity (cpAAI > 85 %) and 16S rRNA gene sequence similarity (>96 %) when compared to other members of the genus confirm the position of these two strains as part of the Agrobacterium genus. They are therefore described as Agrobacterium divergens sp. nov. Besides, our comparative genomic study and survey for clade-specific markers resulted in the discovery of conserved proteins that provide insights into the functional evolution of this genus.
期刊介绍:
Systematic and Applied Microbiology deals with various aspects of microbial diversity and systematics of prokaryotes. It focuses on Bacteria and Archaea; eukaryotic microorganisms will only be considered in rare cases. The journal perceives a broad understanding of microbial diversity and encourages the submission of manuscripts from the following branches of microbiology: