Genome sequencing endophytes from grapevine. Enterobacter ludwigii strain:LecVs2

Plant pathogens and endophytes co-exist and often interact with the host plant and within its microbial community. The outcome of these interactions may lead to healthy plants or to disease, through the inducible production of molecules known as virulence factors. Unravelling the role of endophytes in the expression of virulence may crucially improve our understanding of host-associated microbial communities and their correlation with host health. Virulence is the outcome of a complex network of interactions, and drawing the line between pathogens and endophytes has proven to be conflictive, as strain-level differences in niche overlapping, ecological interactions, state of the host’s immune system and environmental factors are seldom taken into account. Defining genomic the differences at the genomic level between endophytes and plant pathogens is decisive for understanding the boundaries between these two groups. Here we describe the major differences at the genomic level between a seven grapevine endophytic test bacteria, and reference strains. We describe the virulence factors detected in the genomes of the test group, as compared to non-endophytic references, to better understand the distribution of these traits in endophytic genomes. To do this, we adopted a comparative whole-genome approach, encompassing BLAST-based searches through the GUI-based tools Mauve and the artemis comparison tool, ACTBRIG. We also outline divergences in metabolic pathways of these endophytes and reference strains, with the aid of the online platform RAST. We present a summary of the major differences that help drawing the boundaries between harmless and harmful bacteria, in the spirit of contributing to a microbiological definition of endophyte.