Ancestral genome estimation reveals the history of ecological diversification inAgrobacterium

Abstract

Horizontal gene transfer (HGT) is considered as a major source of innovation in bacteria, and as such is expected to drive adaptation to new ecological niches. However, among the many genes acquired through HGT along the diversification history of genomes, only a fraction may have actively contributed to sustained ecological adaptation. We used a phylogenetic approach accounting for the transfer of genes (or groups of genes) to estimate the history of genomes in Agrobacterium biovar 1, a diverse group of soil and plantdwelling bacterial species. We identified clade-specific blocks of co-transferred genes encoding coherent biochemical pathways that may have contributed to the evolutionary success of key Agrobacterium clades.This pattern of gene co-evolution rejects a neutral model of transfer, in which neighbouring genes would be transferred independently of their function and rather suggests purifying selection on collectively coded acquired pathways. The acquisition of these synapomorphic blocks of co-functioning genes probably drove the ecological diversification of Agrobacterium and defined features of ancestral ecological niches, which consistently hint at a strong selective role of host plant rhizospheres.

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

“…vitis sensu stricto and All. ampelinum occurred on chromids and plasmids, suggesting that these replicons may be an important part of the species' adaptive core genome, as previously observed in A. tumefaciens species complex (Lassalle et al, 2017). Ecological differentiation of the two main species of the complex seems to rely on consumption of different nutrient sources, including polyamines and nickel ion (potentially as a key cofactor of ecologically important enzymes) for All.…”

“…was initially considered a single species, but was later designated as a species complex comprising closely related, but distinct genomic species. Several studies applying DDH initially demonstrated this species diversity within Agrobacterium biovar 1 (43)(44)(45), which was later supported by results obtained with AFLP (46,47), housekeeping gene analysis (10,11,14) and whole-genome sequence analysis (30). Although Ophel and Kerr (9) also performed DDH for several All.…”

“…Similarly, Agrobacterium biovar 1 was also initially considered a single species, but was later designated as a species complex comprising divergent genomic species. Several studies applying DDH initially demonstrated species diversity within Agrobacterium biovar 1 (De Ley, 1974, De Ley et al, 1973, Popoff et al, 1984, which was later supported by results obtained with AFLP (Portier et al, 2006, Mougel et al, 2002, housekeeping gene analysis (Costechareyre et al, 2010, Mousavi et al, 2014, Mousavi et al, 2015 and whole genome analysis (Lassalle et al, 2017). Although Ophel and Kerr (1990) also performed DDH for several All.…”

“…These inconsistencies were also observed in another pan-genome phylogeny inferred using parsimony (data not shown). Such limitations of gene content-based phylogenies have previously been reported (30,31).…”

Comparative Genomics of Novel Agrobacterium G3 Strains Isolated From the International Space Station and Description of Agrobacterium tomkonis sp. nov.

“…Further refinement of the taxonomy of Agrobacterium biovar 1, also known as the Agrobacterium tumefaciens species complex, was conducted based on whole-genome information using DDH, leading to the classification of strains into species-level units called genomic species or genomovars (Popoff et al, 1984). This classification framework was later validated and enriched by studies using amplified fragment-length polymorphism (AFLP), marker gene phylogeny, multi-locus sequence analysis (MLSA), comparative genome hybridization (CGH) and core-genome phylogeny (Portier et al, 2006;Costechareyre et al, 2010;Lassalle et al, 2011Lassalle et al, , 2017Mousavi et al, 2015), as recently reviewed by Flores-Felix et al (2020). At the time of writing this communication, the Agrobacterium genus contained 15 named species, of which 11 had validly published names.…”