Complete Genome Sequence of the Barley Pathogen Xanthomonas translucens pv. translucens DSM 18974^T (ATCC 19319^T)

Abstract

We report here the complete 4.7-Mb genome sequence of Xanthomonas translucens pv. translucens DSM 18974^T, which causes black chaff disease on barley (Hordeum vulgare). Genome data of this X. translucens type strain will improve our understanding of this bacterial species.

GENOME ANNOUNCEMENT

The Gram-negative gammaproteobacterium Xanthomonas translucens pv. translucens is the causal agent of a bacterial wilt on Hordeum vulgare (barley) (1) that is often called black chaff. The strain DSM 18974^T (ATCC 19319^T) was isolated from its host plant in Minnesota, USA. It is the type strain of the species X. translucens (2). X. translucens strains occur worldwide and infect a broad range of cereals and forage grasses. At the same time, Xanthomonas strains are applied in biotechnology to synthesize the exopolysaccharide xanthan (3), a commercial thickening agent. Despite gradually rising numbers of publications, our knowledge about X. translucens genomes is still fragmentary. Hence, detailed genome data of X. translucens pv. translucens are suitable to advance functional research and deepen our phylogenetic understanding of X. translucens and related xanthomonads.

Initially, genomic DNA of X. translucens pv. translucens DSM 18974^T was extracted (4) to generate a paired-end library that was shotgun-sequenced with a Genome Sequencer FLX (GS FLX) system by means of the 454 Titanium technology (Roche) as described earlier (5). However, the assembly of the resulting data produced a large number of contigs, possibly pointing to the presence of repetitive IS elements. To address this deficiency, a combination of single-molecule real-time (SMRT) and Illumina sequencing technologies was applied. Genomic DNA was extracted applying Qiagen Genomic-tips 100/G according to the manufacturer’s instructions and sequenced on a PacBio RSII instrument (Pacific Biosciences) using P5 chemistry. Genome assembly was performed with the “RS_HGAP_Assembly.3” protocol included in SMRT Portal version 2.3.0, utilizing 49,791 post-filtered reads with an average read length of 12,646 bp. One complete chromosomal contig was obtained and trimmed, circularized, and adjusted to the beginning of the dnaA gene. To improve the sequence quality, additional genome data were obtained by sequencing a paired-end TruSeq PCR-free DNA fragment library with an average size of 719 ± 226 bp on a MiSeq instrument (Illumina) in a 2 × 300-bp run. This provided a total of 1,021,089,076 bp in 4,490,068 reads, among them 2,129,085 paired-ends reads. The Illumina reads were mapped with the Burrows–Wheeler aligner (6) onto the contig to obtain the consensus sequence of a circular chromosome of 4,715,357 bp with an average coverage of 223× and a G+C content of 67.7%. Automated genome annotation carried out by means of the GenDB platform (7) with the Prodigal gene prediction software (8) revealed 3,736 protein-coding genes, 54 tRNAs, and two rRNA operons.

Comparative analysis employing the EDGAR software (9) facilitated the identification of a CRISPR array in addition to virulence factor genes, which encoded protein-secretion systems like a hrp type III secretion system with transcription activator-like effectors (10) and the polysaccharide xanthan.

Accession number(s).

This whole-genome shotgun project has been deposited in DDBJ/ENA/GenBank under the accession number LT604072. The version described in this paper is the first version, LT604072.1.