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Draft Genome Sequence of Ralstonia solanacearum Strain Rs-T02,
Which Represents the Most Prevalent Phylotype in Guangxi, China
Chengwu Zou, Kaihao Wang, Jiaorong Meng, Gaoqing Yuan, Wei Lin, Haowen Peng, Qiqin Li
College of Agriculture, Guangxi University, Nanning, China
Ralstonia solanacearum strain Rs-T02 was originally isolated from a bacterial wilt of tomato plant in Nanning City of Guangxi
Province, China. It represents the most prevalent phylotype in Guangxi. Here, we present the draft genome sequence of this
strain, which comprises 5,225 genes and 5,976,011 nucleotides with an average GⴙC content of 66.79%. There are 968 different
genes between this isolate and the previously reported genome sequence of Ralstonia solanacearum GMl l000 (race l, biovar 3,
phylotype I), and the genome sequence information of this isolate may be useful for comparative genomic studies to determine
the genetic diversity in this species.
Received 19 February 2016 Accepted 24 February 2016 Published 14 April 2016
Citation Zou C, Wang K, Meng J, Yuan G, Lin W, Peng H, Li Q. 2016. Draft genome sequence of Ralstonia solanacearum strain Rs-T02, which represents the most prevalent
phylotype in Guangxi, China. Genome Announc 4(2):e00241-16. doi:10.1128/genomeA.00241-16.
Copyright © 2016 Zou et al. This is an open-access article distributed under the terms of the Creative Commons Attribution 4.0 International license.
Address correspondence to Qiqin Li, [email protected].
R
alstonia solanacearum (Smith) Yabuuchi et al. (formerly called
Pseudomonas solanacearum) is a soilborne bacterial pathogen
that is a major limiting factor in the production of many crop
plants around the world. This organism is the causal agent of
brown rot of potato; bacterial wilt or southern wilt of tomato,
tobacco, eggplant, and some ornamentals; and Moko disease of
banana (1). Ralstonia solanacearum is a widely distributed pathogen found in tropical, subtropical, and some temperate regions of
the world (2). The species as a whole has a very broad host range
and infects hundreds of species in many plant families. The majority of hosts are dicots, with the major exception being bananas
and plantains. Most economically important host plants are
found in the Solanaceae or nightshade family (3). The specific host
ranges and distributions of Ralstonia solanacearum depend on the
race and to some degree the biovar of the pathogen. These host
ranges and distributions have been changing in recent years. To facilitate a greater understanding of genetic diversity in this species, we
sequenced the genome of Ralstonia solanacearum strain Rs-T02,
which represents the most prevalent phylotype in Guangxi, China.
This strain was isolated from Nanning City of Guangxi Province, China. Gram staining and PCR amplification and sequencing of 16s rRNA genes were used to confirm the isolate as Ralstonia
solanacearum, temporarily named Rs-T02. Genomic DNA was
isolated from culture using a standard genomic DNA purification
protocol (4). Two DNA libraries were constructed: a paired-end
library with an insert size of 500 bp and a mate-pair library with an
insert size of 5 kb. The 500-bp library and the 5-kb library were
sequenced using an Illumina HiSeq2500 with a PE125 strategy to
produce 2,228 Mb of clean data, representing ⬎200-fold coverage
of the genome. Genome assembly was performed using the SOAPdenovo package under default parameters (5, 6). The resulting
draft genome for Ralstonia solanacearum strain Rs-T02 had 15
scaffolds covering 5,976,011 bp, with 66.79% GC content. Genome annotation was performed using the GeneMarkS (http:
//topaz.gatech.edu/GeneMark/), with which 5,225 putative
March/April 2016 Volume 4 Issue 2 e00241-16
protein-coding genes were predicted. tRNAs (60 tRNA sequences) were identified using tRNAscan-SE (7); rRNA genes (4
5S rRNAs, 5 16S rRNAs, and 4 23S rRNAs) were predicted with
rRNAmmer (8); and small RNAs (sRNAs) (0 sRNA sequence)
were predicted by the BLAST against the Rfam (9) database. Comparison of this genome (using MUMmer and LASTZ) to that
of Ralstonia solanacearum GMll000 (race l, biovar3, phylotype I)
(GenBank accession numbers NC_003295.1 and NC_003296.1)
revealed 100 deletions, 75 insertions, and 228 inversions, indicating that there is substantial genetic diversity. Further analysis of
this genome in comparison to other sequenced Ralstonia solanacearum genomes may provide insight into the genetic diversity in this species.
Nucleotide sequence accession numbers. This whole-genome
shotgun project has been deposited at DDBJ/EMBL/GenBank under the accession number LKVH00000000. The version described
in this paper is version LKVH01000000.
ACKNOWLEDGMENT
Library construction and sequencing were performed at the Beijing Novogene Bioinformatics Technology Co., Ltd., China.
FUNDING INFORMATION
This work, including the efforts of Qiqin Li, was funded by National
Natural Science Foundation of China (NSFC) (31460459).
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