Defining the rhizobium leguminosarum species complex

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  • J. Peter W. Young, University of York
  • ,
  • Sara Moeskjær
  • ,
  • Alexey Afonin, All-Russia Institute of Agricultural Microbiology (ARRIAM)
  • ,
  • Praveen Rahi, National Centre for Cell Science
  • ,
  • Marta Maluk, The James Hutton Institute
  • ,
  • Euan K. James, The James Hutton Institute
  • ,
  • Maria Izabel A. Cavassim, University of California at Los Angeles
  • ,
  • M. Harun Or Rashid, Bangladesh Institute of Nuclear Agriculture
  • ,
  • Aregu Amsalu Aserse, University of Helsinki
  • ,
  • Benjamin J. Perry, University of Otago
  • ,
  • En Tao Wang, Instituto Politecnico Nacional
  • ,
  • Encarna Velázquez, Universidad de Salamanca
  • ,
  • Evgeny E. Andronov, All-Russia Institute of Agricultural Microbiology (ARRIAM)
  • ,
  • Anastasia Tampakaki, Agricultural University of Athens
  • ,
  • José David Flores Félix, University of Beira Interior
  • ,
  • Raúl Rivas González, Universidad de Salamanca
  • ,
  • Sameh H. Youseif, Agricultural Research Center
  • ,
  • Marc Lepetit, Universite Cote d'Azur
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  • Stéphane Boivin, Laboratoire des Symbioses Tropicales et Méditerranéennes
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  • Beatriz Jorrin, University of Oxford
  • ,
  • Gregory J. Kenicer, Royal Botanic Garden Edinburgh
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  • Álvaro Peix, Universidad de Salamanca
  • ,
  • Michael F. Hynes, University of Calgary
  • ,
  • Martha Helena Ramírez-Bahena, Universidad de Salamanca
  • ,
  • Arvind Gulati, CSIR - Institute of Himalayan Bioresource Technology
  • ,
  • Chang Fu Tian, China Agricultural University

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.

OriginalsprogEngelsk
Artikelnummer111
TidsskriftGenes
Vol/bind12
Nummer1
Antal sider26
ISSN2073-4425
DOI
StatusUdgivet - jan. 2021

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