Phylogenomic analysis reveals the basis of adaptation of <i>Pseudorhizobium</i> species to extreme environments

Lassalle, Florent; Smm, Dastgheib; Zhao, Fang‐Jie; Zhang, J; Verbarg, Susanne; Frühling, Anja; Brinkmann, Henner; Osborne, T.; Sikorski, Johannes; Balloux, François; Didelot, Xavier; Jm, Santini; Petersen, Jörn

doi:10.1101/690347

Cited by 4 publications

(5 citation statements)

References 49 publications

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“…Many strains in the basal clades of this phylogeny have featured in previous studies that classified them in genera related to, but distinct from, Rhizobium , and this allowed us to identify the main clades as Allorhizobium [ 84 , 85 ] , Neorhizobium [ 85 , 86 ] , Pseudorhizobium [ 87 , 88 ] , Agrobacterium [ 89 ] , Mycoplana [ 90 ] , Pararhizobium [ 85 ] , and an unnamed genus-level clade identified in GTDB as g__Rhizobium_A, which includes the type strains of Rhizobium rhizoryzae and Allorhizobium pseudoryzae . It should be emphasized that the only strains of these genera that are shown in Figure 1 are those that are misclassified as Rhizobium in the NCBI database.…”

Section: Resultsmentioning

confidence: 99%

Defining the Rhizobium leguminosarum Species Complex

Young

Moeskjær

Afonin³

et al. 2021

Genes

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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.

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Section: Resultsmentioning

confidence: 99%

Defining the Rhizobium leguminosarum Species Complex

Young

Moeskjær

Afonin³

et al. 2021

Genes

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“…Further pangenome analyses were conducted using the Pantagruel pipeline under the default settings as described previously (Lassalle et al, 2019, Lassalle et al, 2020) and on the program webpage http://github.com/flass/pantagruel/. Because of computationally highly intensive tasks, the dataset analyzed was limited to the Allorhizobium genus and Rhizobium aggregatum complex (total of 28 strains).…”

Section: Methodsmentioning

confidence: 99%

Genomic analysis provides novel insights into diversification and taxonomy ofAllorhizobium vitis(i.e.Agrobacterium vitis)

Kuzmanović

Biondi

Overmann

et al. 2020

Preprint

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Allorhizobium vitis (formerly named Agrobacterium vitis or Agrobacterium biovar 3) is the primary causative agent of crown gall disease of grapevine worldwide. Whole-genome sequence comparisons and phylogenomic analysis of various All. vitis strains clearly indicated that All. vitis is not a single species, but represents a species complex composed of at least four genomic species. Thus, we amended the description of All. vitis which now refers to a restricted group of strains within the All. vitis complex (i.e. All. vitis sensu stricto) and proposed a description of a novel species All. ampelinum sp. nov. The type strain of All. vitis sensu stricto remains the existing type strain of All. vitis, K309T (= NCPPB 3554T =HAMBI 1817T = ATCC 49767T = CIP 105853T = ICMP 10752T = IFO 15140T = JCM 21033T = LMG 8750T = NBRC 15140T). The type strain of All. ampelinum sp. nov. is S4T (= DSM 112012T = ATCCBAA-846T). This genome-based classification was supported by differentiation of strains based on a MALDI-TOF MS analysis. We also identified gene clusters specific for All. vitis species complex, All. vitis sensu stricto and All. ampelinum, and attempted to predict their function and their role in ecological diversification of these clades, some of which were experimentally validated. Functions of All. vitis species complex-specific genes convergently indicate a role in adaptation to different stresses, including exposure to aromatic compounds. Similarly, All vitis sensu stricto-specific genes also confer the ability to degrade 4-hydroxyphenylacetate and a putative compound related to gentisic acid, while All. ampelinum-specific genes have putative functions related to polyamine metabolism and nickel assimilation. This suggests that these species have differentiated ecologies, each relying on specialized nutrient consumption or toxic compound degradation to adapt to their respective niche. Moreover, our genome-based analysis indicated that Allorhizobium and the “R. aggregatum complex” represent separate genera of the family Rhizobiaceae.

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“…Many strains in the basal clades of this phylogeny have featured in previous studies that classified them in genera related to, but distinct from Rhizobium, and this allowed us to identify the main clades as Allorhizobium [82,83], Neorhizobium [83,84], Pseudorhizobium [85,86], Agrobacterium [87], Mycoplana [88], Pararhizobium [83], and an unnamed genus-level clade identified in GTDB as g__Rhizobium_A, which includes the type strains of Rhizobium rhizoryzae and Allorhizobium pseudoryzae. It should be emphasised that the only strains of these genera that are shown in Figure 1 are those that are misclassified as Rhizobium in the NCBI database.…”

Section: The Genus Rhizobium and Related Generamentioning

confidence: 98%

Defining the Rhizobium Leguminosarum Species Complex

Young¹,

Moeskjær²,

Afonin³

et al. 2020

Preprint

View full text Add to dashboard Cite

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 around 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 characterise 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 characterising the diversity of bacteria, and that taxonomic conclusions should be based on all available genome sequences, not just those of type strains.

show abstract

Phylogenomic analysis reveals the basis of adaptation of Pseudorhizobium species to extreme environments

Cited by 4 publications

References 49 publications

Defining the Rhizobium leguminosarum Species Complex

Defining the Rhizobium leguminosarum Species Complex

Genomic analysis provides novel insights into diversification and taxonomy ofAllorhizobium vitis(i.e.Agrobacterium vitis)

Defining the Rhizobium Leguminosarum Species Complex

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