Phytopathogenic enterobacteria cause economically significant losses of ornamental and crop plants worldwide. Abundant genome sequences for the family as a whole provide rich data to investigate the evolutionary events associated with specialization in animal and plant hosts. Genes acquired by horizontal transfer in the ancestral lineages leading to phytopathogens are high priority targets for experimental characterization as potential contributors to plant-microbe interactions.
Ortholog groups of for all proteins from 307 genomes of enterobacteria were predicted with OrthMCL and used for species tree reconstructions using RAxML, ASTRAL, PhyloNet and SNaQ. Ancestral state reconstructions (ML, parsimony and ad hoc) were used to transform ortholog presence/absence data to predictions of gene gains and losses in the most recent common ancestral lineages of the phytopathogen clades. We integrated these analyses with gene expression profiles, protein annotations, and a database of genes involved with host-microbe interactions.
This study reveals a dominant phylogeny with two distinct clades of phytopathogens. The ancestral lineages leading to the soft rot-associated and Yersinia clades appear to have exchanged substantial numbers of homologous genes, providing evidence that horizontal gene transfer is not randomly distributed among taxa throughout the tree. Focused exchange between lineages can be a major barrier to robust species tree reconstruction and may explain inconsistencies observed in previous phylogenetic analyses. Inferences of gene gains/losses identified hundreds or thousands of genes acquired in the most recent common ancestral lineages leading to the soft rot clade. Integrated analyses of gene flux and functional genomics data prioritizes candidates for further experimentation and suggest that expansion of chemotaxis receptor and ABC transporter protein families through both horizontal transfer and duplication preceded diversification of the soft rot clade.
Despite a clearly reticulate evolutionary history, reconstruction of gene losses and gains in a relatively old lineage provides insight into specialization in plant hosts.