Comparative genomics and transcriptomics of plant-pathogenic xanthomonads – XANTHOMIX

The project XANTHOMIX aims at providing genomic and transcriptomic resources for a better understanding of the infection process, host and tissue specialization, evolutionary history and epidemiology of five Xanthomonas species. Xanthomonads are gram-negative bacteria which cause diseases of more than 400 different host plants belonging to both monocots and dicots, many of them having great economic importance (e.g. barley, rye, wheat, rice, beans, cabbage, cassava, citrus and cotton). Xanthomonads display a high degree of host and tissue specificity. The genus Xanthomonas is an excellent model to study the molecular, evolutionary and epidemiological aspects of host-bacteria interaction.

We wish to sequence 22 strains of Xanthomonas which serve as models in our labs to study all phases of the infection process and/or which are of special importance as quarantine organisms that represent a significant threat for agriculture and global food security.

All chosen strains belong to genetic lineages for which no genomic or transcriptomic data are available, among them two new species and 14 new pathovars. Yet, due to the close genetic relationship of carefully selected strains comparative analyses will allow to discover candidate components responsible for tissue and/or host specificity.

We will use next-generation sequencing technology. Specifically, we will combine 454 sequencing of genomic DNA with Illumina sequencing of cDNA. This combination will allow to obtain high-quality draft genome sequences and at the same time to study the transcriptome under different conditions. cDNAs will be generated from bacteria grown under standard conditions and under conditions that mimic important steps of the plant infection process. Comparison of data will allow to formulate hypotheses about regulons which can easily be tested thanks to the available genome sequences.

For cDNA synthesis, we will use specific protocols which will allow us to identify small, non-coding RNAs and anti-sense RNAs, in addition to the mRNA pool. Knowledge of the transcription start sites will be generated and help to identify regulatory cis-acting promoter elements, riboswitches and translation initiation codons. The plethora of information will lead to excellent structural annotation of these and other, already available genome sequences of Xanthomonas. Expert functional annotation of genes involved in the infection process will generate an invaluable resource for the international scientific community.

Genome-/transcriptome-derived hypotheses about the role of new components of the infection process will be complemented by functional analyses. Our new genomic resources will also be used to develop high-resolution molecular typing tools which will serve in the epidemiological surveillance of these important pathogens.

The project involves four French partners from institutes being active in fundamental and applied research. Researchers involved in this project, mainly belonging to IRD, CIRAD and INRA, are all well recognized as experts in their field (microbiology, plant pathology, phylogeny, genetics, genomics, epidemiology) with a broad expertise in genetics, genomics and epidemiology of pathogenic bacteria with particular expertise on the Xanthomonas genus.