Defining the Rhizobium leguminosarum Species Complex

J. Peter W. Young (Lead / Corresponding author), Sara Moeskjær, Alexey Afonin, Praveen Rahi, Marta Maluk, Euan K. James, Maria Izabel A. Cavassim, M. Harun-Or Rashid, Aregu Amsalu Aserse, Benjamin J. Perry, En Tao Wang, Encarna Velázquez, Evgeny E. Andronov, Anastasia Tampakaki, José David Flores Félix, Raúl Rivas González, Sameh H. Youseif, Marc Lepetit, Stéphane Boivin, Beatriz JorrinGregory J. Kenicer, Álvaro Peix, Michael F. Hynes, Martha Helena Ramírez-Bahena, Arvind Gulati, Chang-Fu Tian

Research output: Contribution to journalArticlepeer-review

41 Citations (Scopus)
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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.

Original languageEnglish
Article number111
Number of pages26
Issue number1
Publication statusPublished - 18 Jan 2021


  • DNA, Bacterial/genetics
  • Genome, Bacterial
  • Phylogeny
  • Rhizobium leguminosarum/classification
  • Sequence Analysis, DNA
  • Average nucleotide identity
  • Genospecies
  • Bacterial taxonomy
  • Rhizobium
  • Core genes
  • Species complex
  • Housekeeping genes
  • Speciation

ASJC Scopus subject areas

  • Genetics(clinical)
  • Genetics


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