Genome Sequence of the Tobacco Bacterial Wilt Pathogen Ralstonia solanacearum

Abstract

Ralstonia solanacearum is a causal agent of plant bacterial wilt with thousands of distinct strains in a heterogeneous species complex. Here we report the genome sequence of a phylotype IB strain, Y45, isolated from tobacco (Nicotiana tabacum) in China. Compared with the published genomes of eight strains which were isolated from other hosts and habitats, 794 specific genes and many rearrangements/inversion events were identified in the tobacco strain, demonstrating that this strain represents an important node within the R. solanacearum complex.

GENOME ANNOUNCEMENT

Ralstonia solanacearum is a phytopathogenic bacterium with an unusually broad host range and a wide geographical distribution (1). It causes a wilt disease with deadly effects in many economically important crops like tomato, potato, tobacco, and banana (1, 5). Understanding the characteristics of R. solanacearum strains is helpful to determine the way to prevent or reduce potential economic losses. So far, eight genomes of R. solanacearum strains from three hosts (tomato, potato, and geranium) with a variety of habitats have been sequenced (6, 8, 14, 16, 19). Owing to the significant genomic variations of R. solanacearum strains derived from different regions and hosts, a strain (Y45) isolated from tobacco in Yunnan Province, China, was sequenced, annotated, and compared to the other eight strains. It is the first R. solanacearum strain isolated in East Asia.

Contigs and scaffolds were assembled and aligned using SOAPdenovo 1.05 (11) and SOAPaligner (10). Protein-coding and other genes were predicted by Glimmer3.0, rRNAmmer, tRNAscan, and Rfam (4, 7, 9, 17). Repetitive elements were identified by RepeatMasker (http://www.repeatmasker.org) and Tandem Repeat Finder (2). Phylogenetic and genomic analyses were carried out using MEGA4 based on egl and hrpB sequences (13, 18) and Mauve (15).

A total of 1,067.5 Mb clean data from two different insert size libraries (500 bp and 2 kb) were generated for strain Y45 using the Illumina HiSeq2000 paired-end strategy and assembled into 46 scaffold sequences (90% of the assembly falls into 10 scaffolds lager than 142 kb) with a length of approximately 5.73 Mb, representing 98.5% of the genome, whose size was estimated to be 5.82 Mb using the 17-mer approach (GSP; http://gsizepred.sourceforge.net/) (3, 12). Compared with the well-documented genome of strain GMI1000 (16), the 46 segments could be divided into three parts, including a chromosome segment (3,726,478 bp), a megaplasmid segment (1,985,910 bp), and sequences which were not assigned to either of the two circular replicons, suggesting their uniqueness to this strain (17,900 bp). In all, 5,496 coding sequences, 53 tRNAs, and 5 rRNAs were predicted in the genome, respectively. Moreover, 14,472-bp transposable elements and 43,648-bp tandem repeats were predicted, comprising 0.25% and 0.76% of the genome, respectively. Of the 5,496 genes, 4,864 could produce a hit in at least one of the public protein databases (BLASTP e value, ≤1e-5); 632 genes, however, did not match any known proteins in the current public databases. In a comparative genome analysis with the eight sequenced R. solanacearum strains, 794 specific genes were identified within the genome of strain Y45, most of which are of unknown function or encode hypothetical proteins. Notably, genomic alignments revealed many rearrangements and inversions between strain Y45 (phylotype IB, according to our phylogenetic analysis) and the other strains, which occurred since Y45 separated from the other strains. Thus, the genome of strain Y45 represents a unique phylogenetic node and provides invaluable information for R. solanacearum genomic research.

Nucleotide sequence accession numbers.

This Whole Genome Shotgun project has been deposited at DDBJ/EMBL/GenBank under accession no. AFWL00000000. The version described in this paper is the first version and is available under accession no. AFWL01000000.