Draft Genome Sequence of Entomopathogenic Bacterium Photorhabdus temperata Strain M1021, Isolated from Nematodes Gun-Seok Park,a Abdur Rahim Khan,a Sung-Jun Hong,a Eun-Kyung Jang,b Ihsan Ullah,a Byung Kwon Jung,a JungBae Choi,a Na-Kyung Yoo,c Keun-Joon Park,c Jae-Ho Shina School of Applied Biosciences, Kyungpook National University, Daegu, South Koreaa; Food and Biological Resources Examination Division, Korean Intellectual Property Office, Daejeon, South Koreab; Lifetechnologies Korea, LLC, NGS Field Application Specialist Team, Seoul, South Koreac
Photorhabdus temperata strain M1021 is an entomopathogenic bacterium belonging to the family Enterobacteriaceae and is symbiotically associated with nematodes. The draft genome sequence of P. temperata strain M1021 consists of 5,598,253 bp with a GⴙC content of 43.7%, and it has 6,120 protein-coding genes. Received 20 August 2013 Accepted 21 August 2013 Published 12 September 2013 Citation Park G-S, Khan AR, Hong S-J, Jang E-K, Ullah I, Jung BK, Choi J, Yoo N-K, Park K-J, Shin J-H. 2013. Draft genome sequence of entomopathogenic bacterium Photorhabdus temperata strain M1021, isolated from nematodes. Genome Announc. 1(5):e00747-13. doi:10.1128/genomeA.00747-13. Copyright © 2013 Park et al. This is an open-access article distributed under the terms of the Creative Commons Attribution 3.0 Unported license. Address correspondence to Jae-Ho Shin,
[email protected].
T
he genus Photorhabdus, within the class Gammaproteobacteria and the family Enterobacteriaceae, currently includes species that are lethal pathogens of insects (1). Photorhabdus species live in a mutualistic association with entomopathogenic nematodes of the family Heterorhabditidae and are released from the gut of the nematode upon invasion into the insect hemocoel (2). The bacteria multiply and kill the host within 24 to 48 h because of the toxins produced by Photorhabdus bacteria, known as insecticidal toxin complex proteins (Tc), which exhibit oral as well as hemocoel toxicity (3). Three Tc components are required for full toxicity: TcdA-like, TcdB-like, and TccC-like components. Other toxins, including “makes caterpillars floppy” toxins (Mcf1 and Mcf2) promote the rapid destruction of the insect midgut, resulting in “floppy” caterpillars that suffer from a loss of body turgor (4). The Photorhabdus insect-related toxins (PirAB) are shown to be binary toxins with injectable and oral activity toward several species of insects (5). P. temperate strain M1021 was identified and characterized by Jang et al. (6). The genome of this strain has been sequenced via the Ion Torrent Personal Genome Machine (PGM) sequencer system using a 316D sequencing chip (7). The sequence was assembled using MIRA 3.4.0. The assembled genome consists of 298 contigs (⬎418 bp), with a genome size of 5,598,253 bp at 31.50-fold coverage and a G⫹C content of 43.7%. The assembled contigs were submitted to the RAST annotation server (http://rast .nmpdr.org/) for subsystem classification and functional annotation. A total of 6,120 protein-coding sequences (CDS) were predicted, with 47% assigned to recognizable functional genes. There are 76 ribosomal genes, of which 71 are tRNAs and 1 and 4 are 16S and 23S rRNAs, respectively. The complete gene cluster of insecticidal genes was predicted from the genome sequence. The genes for insecticidal proteins, such as TccA, TccB, TccC, and Mcf, have toxicity when injected into insects (E.-K. Jang, I. Ullah, S.-J. Hong,
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G.-S. Park, J.-H. Shin, unpublished data). Also, we studied phytohormone production and phosphate solubilization in P. temperata M1021 to produce the phytohormone indole-3acetic acid (IAA) (8). Knowledge of the P. temperata M1021 genome sequence will improve our understanding of insecticidal toxicity. Nucleotide sequence accession number. The draft genome sequence of P. temperata strain M1021 has been included in the GenBank Whole-Genome Shotgun (WGS) database under the accession no. AUXQ00000000. The version described in this paper is the first version. ACKNOWLEDGMENT 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).
REFERENCES 1. Bowen D, Rocheleau TA, Blackburn M, Andreev O, Golubeva E, Bhartia R, Ffrench-Constant RH. 1998. Insecticidal toxins from the bacterium Photorhabdus luminescens. Science 280:2129 –2132. 2. Joyce SA, Watson RJ, Clarke DJ. 2006. The regulation of pathogenicity and mutualism in Photorhabdus. Curr. Opin. Microbiol. 9:127–132. 3. Münch A, Stingl L, Jung K, Heermann R. 2008. Photorhabdus luminescens genes induced upon insect infection. BMC Genomics 9:229. doi:10.1186/1 471-2164-9-229. 4. Waterfield NR, Daborn PJ, Ffrench-Constant RH. 2004. Insect pathogenicity islands in the insect pathogenic bacterium Photorhabdus. Physiol. Entomol. 29:240 –250. 5. Yang G, Dowling AJ, Gerike U, ffrench-Constant RH, Waterfield NR. 2006. Photorhabdus virulence cassettes confer injectable insecticidal activity against the wax moth. J. Bacteriol. 188:2254 –2261. 6. Jang EK, Ullah I, Lim JH, Lee IJ, Kim JG, Shin JH. 2012. Physiological and molecular characterization of a newly identified entomopathogenic bacteria, Photorhabdus temperata M1021. J. Microbiol. Biotechnol. 22: 1605–1612.
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Park et al.
7. Rothberg JM, Hinz W, Rearick TM, Schultz J, Mileski W, Davey M, Leamon JH, Johnson K, Milgrew MJ, Edwards M, Hoon J, Simons JF, Marran D, Myers JW, Davidson JF, Branting A, Nobile JR, Puc BP, Light D, Clark TA, Huber M, Branciforte JT, Stoner IB, Cawley SE, Lyons M, Fu Y, Homer N, Sedova M, Miao X, Reed B, Sabina J, Feierstein E, Schorn M, Alanjary M, Dimalanta E, Dressman D, Kasinskas R, Sokolsky
2 genomea.asm.org
T, Fidanza JA, Namsaraev E, McKernan KJ, Williams A, Roth GT, Bustillo J. 2011. An integrated semiconductor device enabling non-optical genome sequencing. Nature 475:348 –352. 8. Ullah I, Khan A, Park G-S, Lim J-H, Waqas M, Lee I-J, Shin J-H. 2013. Analysis of phytohormones and phosphate solubilization in Photorhabdus spp. Food Sci. Biotechnol. 22:25–31.
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