Defining the Rhizobium leguminosarum Species Complex

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Young , J P W , Moeskjaer , S , Afonin , A , Rahi , P , Maluk , M , James , E K , Cavassim , M I A , Rashid , M H , Aserse , A A , Perry , B J , Wang , E T , Velazquez , E , Andronov , E E , Tampakaki , A , Flores Felix , J D , Rivas Gonzalez , R , Youseif , S H , Lepetit , M , Boivin , S , Jorrin , B , Kenicer , G J , Peix , A , Hynes , M F , Ramirez-Bahena , M H , Gulati , A & Tian , C-F 2021 , ' Defining the Rhizobium leguminosarum Species Complex ' , Genes , vol. 12 , no. 1 , 111 .

Title: Defining the Rhizobium leguminosarum Species Complex
Author: Young, J. Peter W.; Moeskjaer, Sara; Afonin, Alexey; Rahi, Praveen; Maluk, Marta; James, Euan K.; Cavassim, Maria Izabel A.; Rashid, M. Harun-or; Aserse, Aregu Amsalu; Perry, Benjamin J.; Wang, En Tao; Velazquez, Encarna; Andronov, Evgeny E.; Tampakaki, Anastasia; Flores Felix, Jose David; Rivas Gonzalez, Raul; Youseif, Sameh H.; Lepetit, Marc; Boivin, Stephane; Jorrin, Beatriz; Kenicer, Gregory J.; Peix, Alvaro; Hynes, Michael F.; Ramirez-Bahena, Martha Helena; Gulati, Arvind; Tian, Chang-Fu
Contributor: University of Helsinki, Ecosystems and Environment Research Programme
Date: 2021-01
Language: eng
Number of pages: 26
Belongs to series: Genes
ISSN: 2073-4425
Abstract: Bacteria currently included in Rhizobium leguminosarum are too diverse to be considered a single species, so we can refer to this as a species complex (the Rlc). We have found 429 publicly available genome sequences that fall within the Rlc and these show that the Rlc is a distinct entity, well separated from other species in the genus. Its sister taxon is R. anhuiense. We constructed a phylogeny based on concatenated sequences of 120 universal (core) genes, and calculated pairwise average nucleotide identity (ANI) between all genomes. From these analyses, we concluded that the Rlc includes 18 distinct genospecies, plus 7 unique strains that are not placed in these genospecies. Each genospecies is separated by a distinct gap in ANI values, usually at approximately 96% ANI, implying that it is a 'natural' unit. Five of the genospecies include the type strains of named species: R. laguerreae, R. sophorae, R. ruizarguesonis, "R. indicum" and R. leguminosarum itself. The 16S ribosomal RNA sequence is remarkably diverse within the Rlc, but does not distinguish the genospecies. Partial sequences of housekeeping genes, which have frequently been used to characterize isolate collections, can mostly be assigned unambiguously to a genospecies, but alleles within a genospecies do not always form a clade, so single genes are not a reliable guide to the true phylogeny of the strains. We conclude that access to a large number of genome sequences is a powerful tool for characterizing the diversity of bacteria, and that taxonomic conclusions should be based on all available genome sequences, not just those of type strains.
Subject: Rhizobium
species complex
bacterial taxonomy
core genes
housekeeping genes
average nucleotide identity
1184 Genetics, developmental biology, physiology

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