High-Quality Draft Genome Sequence of Xanthomonas alfalfae subsp. alfalfae Strain CFBP 3836.

We report the high-quality draft genome sequence of Xanthomonas alfalfae subsp. alfalfae strain CFBP 3836, the causal agent of bacterial leaf and stem spot in lucerne (Medicago sativa). Comparative genomics will help to decipher the mechanisms provoking disease and triggering the defense responses of this pathogen of the model legume Medicago truncatula.

GENOME ANNOUNCEMENT

Xanthomonas alfalfae subsp. alfalfae (formerly Xanthomonas axonopodis pv. alfalfae) is the causal agent of bacterial leaf and stem spot of lucerne (Medicago sativa) (1, 2). While lucerne is the main host of X. alfalfae subsp. alfalfae, other hosts, such as soybean (Glycine max), clover (Trifolium spp.), and vetch (Vicia spp.), have been reported (3). X. alfalfae subsp. alfalfae is also pathogenic on the model legume Medicago truncatula (4). Lesions first appear on the leaf as water-soaked spots surrounded by a diffuse chlorotic area, which then turns dry, yellow-brown, and papery. Severe defoliation is a common result of leaf infection. Postemergence damping off, stunting of seedlings, and damage of lucerne stands are other symptoms. This seed-borne disease may cause severe losses in hot, moist environments (3). To better understand the molecular basis of legume-bacterium interactions, we sequenced the genome of the X. alfalfae subsp. alfalfae strain CFBP 3836. This strain is the pathotype strain of the former pathovar X. axonopodis pv. alfalfae (5). This strain originates from the Sudan (http://www.angers-nantes.inra.fr/cfbp/resultnum_e.php?r0=3836).

This genome was sequenced using the Illumina HiSeq 2000 platform (GATC Biotech, Germany). Shotgun sequencing yielded 116,576,062 read pairs (37,799,928 100-bp paired-end reads with an insert size of ca. 250 bp and 78,776,134 bp mate-pair reads with an insert size of approximately 3 kb). A combination of Velvet (6), SOAPdenovo, and SOAP Gapcloser (7) yielded 22 contigs >500 bp (N50, 763,181 bp), with the largest contig being 2,433,808 bp, for a total assembly size of 5,077,532 bp. Multilocus sequence analyses of seven housekeeping genes described earlier for xanthomonads confirmed that strain CFBP 3836 belongs to X. alfalfae subsp. alfalfae (8).

The genome carries the core characteristics shared by most plant-pathogenic xanthomonads, including chemotaxis- and flagellum-encoding genes, many genes encoding two-component systems, and TonB-dependent transporters. This genome sequence displays the genes coding for the six secretion systems (from T1SS to T6SS) that have been identified so far in Gram-negative bacteria and multiple effectors. A minimum repertoire of 23 type III effectors is predicted. It comprises two putative transcription activator-like effectors, the highly repetitive sequence of which could not be completely resolved with this sequencing strategy. This genome sequence will be a valuable tool for transcriptomic and genetic studies to allow for a better understanding of disease development and plant defense triggering in legume-bacterium interactions.

Nucleotide sequence accession numbers.

This whole-genome shotgun project has been deposited in GenBank under the accession no. AUWN00000000. The version described in this paper is the first version, AUWN01000000.