Genome Sequence of Ralstonia Solanasearum Virulent

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Genome Sequence of an Avirulent Strain of Ralstonia solanasearum
FJAT-1458
Xuefang Zhenga,b, Bo Liua, Yingzhi Lina,Weiqi Tangc, Jianmei Chea,Yujing Zhua, and Naiquan Linb
Agricultural Bio-resource Institute, Fujian Academy of Agricultural Sciences, Fuzhou, Fujian, People’s Republic of China a;
Biological Control Institute, Fujian Agricultural and Forest University, Fuzhou, Fujian, People’s Republic of China b; and Life
science college, Fujian Agricultural and Forest University, Fuzhou, Fujian, People’s Republic of Chinac
E-mail: Xuefang zheng [email protected], Weiqi Tang [email protected], Bo Liu [email protected],
Yujing Zhu [email protected], Jianmei Che [email protected], Yingzhi Lin [email protected], Naiquan Lin
[email protected]
The avirulent strain of Ralstonia solanacearum FJAT-1458 was isolated in a healthy tomato plant in the bacteria wilt
disease infected field. The whole genome sequence of strain FJAT-1458 was sequenced using Solexa and was assembled by
hybrid assembly strategy of reference-based and de novo assembly approach. The draft genome sequence of avirulent
strain, R. solanacearum FJAT-1458 was 5.85 Mb in size and consisted of 5991 coding sequences (CDSs) and the G+C
content of whole genome was 66.3%.
Ralstonia solanacearum, a Gram-negative soil borne pathogen responsible for bacterial wilt disease in
many important crops, possessed with different pathogenicity (1). Virulent strains of it could infect host plants
and cause disease, while avirulent strains could also infect host plants wihtout killing the hosts (2). Strain
FJAT-1458 was isolated in a healthy tomato plant in the bacteria wilt disease infected field in Nanping City,
Fujan Province, PR China, and was cultured in TTC medium (1% peptone, 0.1% trypticas, 0.5% glucose, 1.8%
agar and 0.05% 2,3,5-triphenyltetrazolium chloride) at 30℃ for 48h. Based on morphological detection (3), R.
solanacearum special primer PCR analyses (4) and pathogenicity identification (5), the strain FJAT-1458 was
recognized as an avirulent R. solanacearum. In this paper, the whole genome of stain FJAT-1458 was
sequenced to augment genome information, for which, so far, ten genomes of virulent R. solanacearum strains
had been sequenced (6-12). Here, we first report draft genome sequences of an avirulent strain, R.
solanacearum FJAT-1458.
The whole-genome of avirulent R. solanacearum strain FJAT-1458 was sequenced by using Illumina
Genome Analyzer IIx with 300 bp and 2500 bp paired-end libraries. Raw reads were trimmed using modified
Mott algorithm implemented by custom perl script. Contigs and scaffolds were assembled using Velvet 1.2.01
(13). Coding sequences (CDS), rRNA and tRNA were predicted by prodigal 2.60 (14), rRNAmmer (15) and
tRNAscan-SE (16), respectively. Function annotation was based on BLASTp with nonredundant public
databases, NR, Swiss-Prot and trEMBL.
A total of 736Mb high quality data were assembled into 138 scaffolds and 1447 contigs for strain
FJAT-1458, with genome size 5.85 Mb. The N50 of scaffolds and contigs were 287786 bp and 7275 bp
respectively. Compared with the genome of strain GMI1000, contigs were organized in two circular replicons,
including a chromosome and a megaplasmid. The chromosome and the megaplasmid contained 67 and 45
scaffolds, representing 3,875,742 bp and 1,950,760 bp, respectively. Morever, there were 26 scaffolds (19,518
bp) unassigned to either of the two replicans.
The whole G+C content of strain FJAT-1458 genome is 66.3%. The entire genome contains 5,991
predicted CDSs. 54 tRNA genes, and 4 rRNA, respectively. Of the 5,991 CDSs, ??genes (representing ??% of
2
the genome) could produce a hit in at least one of the public protein database; ?? genes(representing ??% f the
genome), however, did not match any known proteins in the current public databases. In comparison of genome
analysis with the ten already-sequenced R. solanacearum virulent strains, 447 strain-specific genes were
identified within the genome of strain FJAT-1458, 37.14% of which fell into three genome regions with sizes
of 34.5kb, 47.1kb and 53.1kb, respectively. The specific genes of strain FJAT-1458 provided valuable
information for pathogenicity identification of R. solanacearum.
Nucleotide sequence accession numbers. This Whole Genome Shotgun project for Ralstonia solanasearum
Avirulent Strain FJAT-1458 has been deposited at DDBJ/EMBL/GenBank under the accession
AHIX00000000. The version described in this paper is the first version.
ACKNOWLEDGMENTS
This work was supported by the Agricultural Bio-resource Institute, Fujian Academy of Agricultural Sciences,
People’s Republic of China. The work was financed by the 948 project (2011-G25) from the Chinese Ministry
of Agriculture as well as earlier by the 973 program research project (2011CB111607), the project of
agriculture science and technology achievement transformation (2010GB2C400220), and the international
cooperation project (2012DFA31120) from the Chinese Ministry of Science and Technology.
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