RT Journal Article SR Electronic T1 Ancestral genome reconstruction reveals the history of ecological diversification in Agrobacterium JF bioRxiv FD Cold Spring Harbor Laboratory SP 034843 DO 10.1101/034843 A1 Florent Lassalle A1 Rémi Planel A1 Simon Penel A1 David Chapulliot A1 Valérie Barbe A1 Audrey Dubost A1 Alexandra Calteau A1 David Vallenet A1 Damien Mornico A1 Thomas Bigot A1 Laurent Guéguen A1 Ludovic Vial A1 Daniel Muller A1 Vincent Daubin A1 Xavier Nesme YR 2016 UL http://biorxiv.org/content/early/2016/10/20/034843.abstract AB 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 implement a reverse ecology approach, involving the phylogenetic reconstruction of the evolutionary history of the pangenome within a bacterial clade and the modelling of the HGT process to recognize adaptive gene gains. We apply it to Agrobacterium biovar 1, a diverse group of soil and plant-dwelling bacterial species. We identify synapomorphic gene gains for major clades and show that most are organized into blocks of co-transferred genes encoding coherent biochemical pathways. This pattern of gene co-evolution rejects a neutral model of transfer, in which neighbouring genes would be transferred independently of their function. Instead, the conservation of acquired genes appears driven by purifying selection on collectively coded functions. We therefore propose synapomorphic blocks of co-functioning genes as candidate determinants of ecological adaptation of each clade. Their inferred biochemical functions define features of ancestral ecological niches, which consistently hint at the strong selective role of host plant rhizospheres.