Open access
12 February 2015

Draft Genome Sequence and Annotation of the Insect Pathogenic Bacterium Xenorhabdus nematophila Strain C2-3, Isolated from Nematode Steinernema carpocapsae in the Republic of Korea


Xenorhabdus nematophila strain C2-3, which belongs to the family Enterobacteriaceae, was isolated from entomopathogenic nematodes collected in the Republic of Korea. Herein, we report a 4.38-Mbp draft genome sequence of X. nematophila strain C2-3, with a 43.6% G+C content. The RAST annotation analysis revealed 4,994 protein-coding sequences in the draft genome.


Xenorhabdus spp. are Enterobacteriaceae, symbiotic bacteria associated with soil nematodes such as Steinernematidae and Heterorhabditidae spp. (1). Entomopathogenic bacteria symbiotically associated with nematodes are of great interest as biocontrol agents against insect pests (2, 3). Xenorhabdus spp. are virulent pathogens synthesizing proteins and other secondary metabolites, such as benzylideneacetone, iodinine, phenethylamides, xenorhabdins, xenorxides, and xenocoumacins, involved in pathogenicity against a wide range of insects (4). Previous studies have revealed numerous secondary metabolitic activities, e.g., antibacterial activity, antifungal activity, insecticidal activity, and cytotoxicity, investigated in other Xenorhabdus strains (5).
In the present study, bacterial strain C2-3 was isolated from nematodes collected in the Republic of Korea. The strain was identified through 16S rRNA sequence comparison, which revealed 99.8% sequence similarity with Xenorhabdus nematophila ATCC 19061, and it was therefore named Xenorhabdus nematophila strain C2-3. Moreover, the identification was confirmed via average nucleotide identity (ANI) values (6). The whole-genome sequence of the C2-3 strain showed 98.9%, 81.9%, 80.8%, and 79.7% ANI values for X. nematophila ATCC 19061 (1), X. szentirmaii DSM16338 (7), and X. bovienii SS-2004 (1), respectively.
The newly identified strain C2-3 was subjected to draft genome sequencing to investigate the presence of insecticidal toxins, secondary metabolites, and antimicrobial compounds. The genomic DNA from X. nematophila C2-3 was extracted using a QIAamp DNA minikit (Qiagen, Hilden, Germany), and the whole genome was sequenced with the Ion Torrent PGM sequencer (Thermo Scientific, Bremen, Germany), using the 316 v2 chip sequencing protocol. A total of 3,310,612 reads were generated, with a mean length 272 bp. The draft genome sequence was assembled de novo using MIRA assembler version 4.0, which generated 284 contigs (500 bp or more), with an N50 contig length of 48,919 bp. The draft genome sequence consists of 4,386,383 bp, with 60-fold genome coverage having approximately 43.6% G+C content.
Subsequent to the assembly, the contigs were submitted to the RAST annotation server ( for subsystem classification and functional annotation (8). The annotation results revealed 4,994 predicted coding sequences, including 67 tRNAs, 32 rRNAs, and 4 noncoding RNAs. In addition, there were two complexes, xptA1/xptB1/xptC1 and xptA2/xptB1/xptC1 (9, 10). These toxin complexes have 47% to 53% amino acid sequence similarity with that of the toxin complex (TC) protein of P. luminescens (11). Moreover, the xptA1 gene encoding central insecticidal toxin, as well as xptB1 and xptC1 genes encoding toxicity enhancer proteins (10), were clustered.
In addition, an antimicrobial gene cluster identified as xcnA-N and related to xenocoumacin production (12) was also revealed. Based on the annotation results, we presume that the genome sequence of X. nematophila strain C2-3 will lead to the discovery of useful genes and gene products for environmentally friendly agriculture applications.

Nucleotide sequence accession numbers.

This whole-genome shotgun project has been deposited at DDBJ/EMBL/GenBank under the accession no. JRJV00000000. The version described in this paper is version JRJV01000000.


This research was supported by the Basic Science Research Program through the National Research Foundation of Korea (NRF), funded by the Ministry of Education (NRF-2013R1A1A2010298).


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Information & Contributors


Published In

cover image Genome Announcements
Genome Announcements
Volume 3Number 126 February 2015
eLocator: e01521-14
PubMed: 25676754


Received: 23 December 2014
Accepted: 30 December 2014
Published online: 12 February 2015



Sung-Jun Hong
School of Applied Biosciences, Kyungpook National University, Daegu, Republic of Korea
Ihsan Ullah
School of Applied Biosciences, Kyungpook National University, Daegu, Republic of Korea
Gun-Seok Park
School of Applied Biosciences, Kyungpook National University, Daegu, Republic of Korea
Byung Kwon Jung
School of Applied Biosciences, Kyungpook National University, Daegu, Republic of Korea
JungBae Choi
School of Applied Biosciences, Kyungpook National University, Daegu, Republic of Korea
Abdur Rahim Khan
School of Applied Biosciences, Kyungpook National University, Daegu, Republic of Korea
Min-Chul Kim
School of Applied Biosciences, Kyungpook National University, Daegu, Republic of Korea
Jae-Ho Shin
School of Applied Biosciences, Kyungpook National University, Daegu, Republic of Korea


Address correspondence to Jae-Ho Shin, [email protected].

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