@article{fdi:010080641,
  title = {{D}efining the {R}hizobium leguminosarum species complex},
  author = {{Y}oung, {J}. {P}. {W}. and {M}oeskjaer, {S}. and {A}fonin, {A}. and {R}ahi, {P}. and {M}aluk, {M}. and {J}ames, {E}. {K}. and {C}avassim, {M}. {I}. {A}. and {R}ashid, {M}. {H}. {O}. and {A}serse, {A}. {A}. and {P}erry, {B}. {J}. and {W}ang, {E}. {T}. and {V}elazquez, {E}. and {A}ndronov, {E}. {E}. and {T}ampakaki, {A}. and {F}elix, {J}. {D}. {F}. and {G}onzalez, {R}. {R}. and {Y}ouseif, {S}. {H}. and {L}epetit, {M}. and {B}oivin, {S}t{\'e}phane and {J}orrin, {B}. and {K}enicer, {G}. {J}. and {P}eix, {A}. and {H}ynes, {M}. {F}. and {R}amirez-{B}ahena, {M}. {H}. and {G}ulati, {A}. and {T}ian, {C}. {F}.},
  editor = {},
  language = {{ENG}},
  abstract = {{B}acteria currently included in {R}hizobium leguminosarum are too diverse to be considered a single species, so we can refer to this as a species complex (the {R}lc). {W}e have found 429 publicly available genome sequences that fall within the {R}lc and these show that the {R}lc is a distinct entity, well separated from other species in the genus. {I}ts sister taxon is {R}. anhuiense. {W}e constructed a phylogeny based on concatenated sequences of 120 universal (core) genes, and calculated pairwise average nucleotide identity ({ANI}) between all genomes. {F}rom these analyses, we concluded that the {R}lc includes 18 distinct genospecies, plus 7 unique strains that are not placed in these genospecies. {E}ach genospecies is separated by a distinct gap in {ANI} values, usually at approximately 96% {ANI}, implying that it is a 'natural' unit. {F}ive of the genospecies include the type strains of named species: {R}. laguerreae, {R}. sophorae, {R}. ruizarguesonis, "{R}. indicum" and {R}. leguminosarum itself. {T}he 16{S} ribosomal {RNA} sequence is remarkably diverse within the {R}lc, but does not distinguish the genospecies. {P}artial 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. {W}e 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.},
  keywords = {{R}hizobium ; species complex ; bacterial taxonomy ; core genes ; housekeeping ; genes ; average nucleotide identity ; speciation ; genospecies},
  booktitle = {},
  journal = {{G}enes},
  volume = {12},
  numero = {1},
  pages = {111 [26 p.]},
  year = {2021},
  DOI = {10.3390/genes12010111},
  URL = {https://www.documentation.ird.fr/hor/fdi:010080641},
}