TY - JOUR T1 - Ancestral genome reconstruction reveals the history of ecological diversification in <em>Agrobacterium</em> JF - bioRxiv DO - 10.1101/034843 SP - 034843 AU - Florent Lassalle AU - Rémi Planel AU - Simon Penel AU - David Chapulliot AU - Valérie Barbe AU - Audrey Dubost AU - Alexandra Calteau AU - David Vallenet AU - Damien Mornico AU - Thomas Bigot AU - Laurent Guéguen AU - Ludovic Vial AU - Daniel Muller AU - Vincent Daubin AU - Xavier Nesme Y1 - 2017/01/01 UR - http://biorxiv.org/content/early/2017/06/12/034843.abstract N2 - Horizontal gene transfer (HGT) is considered a major source of innovation in bacteria, and as such is expected to drive the 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. Here, we use a phylogenetic approach accounting for the transfer of genes (or groups of genes) to reconstruct the history of genomes in Agrobacterium biovar 1, a diverse group of soil and plant-dwelling bacterial species. We identify 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 suggests purifying selection on collectively coded acquired pathways. We argue that these synapomorphic blocks of co-functioning genes which consistently hint at the strong selective role of host plant rhizospheres, have driven the ecological diversification of Agrobacterium and define features of ancestral ecological niches. ER -