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Complete Genome Sequence of Trueperella pyogenes, Isolated from Infected Farmland Goats Su-hui Zhang,a,b Jin-jie Qiu,a Rui Yang,a Ke-fei Shen,a Guo-yang Xu,a Li-zhi Fua,b Chongqing Academy of Animal Sciences, Chongqing, People’s Republic of Chinaa; Chongqing Engineering Research Center for Goat, Chongqing, People’s Republic of Chinab S.-H. Z. and J.-J. Q. contributed equally to this article.
Trueperella pyogenes is a significant pathogen of livestock, causing diverse diseases, such as mastitis, liver abscessation, and pneumonia. In this study, we have reported the genome sequence of Trueperella pyogenes 2012CQ-ZSH. Moreover, several genes coding for virulence factors were found, such as pyolysin (PYO), nanH, nanP, cbpA, fimC, and fimE. Received 24 October 2016 Accepted 25 October 2016 Published 15 December 2016 Citation Zhang S-H, Qiu J-J, Yang R, Shen K-F, Xu G-Y, Fu L-Z. 2016. Complete genome sequence of Trueperella pyogenes, isolated from infected farmland goats. Genome Announc 4(6):e01421-16. doi:10.1128/genomeA.01421-16. Copyright © 2016 Zhang et al. This is an open-access article distributed under the terms of the Creative Commons Attribution 4.0 International license. Address correspondence to Li-zhi Fu,
[email protected].
T
rueperella pyogenes, first named Aeranobacterium pyogenes, was reclassified into the genus Trueperella based on the phylogenetic analysis, according to Nagib et al. (1). T. pyogenes is a commensal and opportunistic pathogen of livestock, causing diverse diseases, such as mastitis, liver abscessation, and pneumonia. T. pyogenes expresses several main virulence factors that help it to infect diverse animals, including pyolysin (PLO), nanH, nanP, fimA, and cpbA (2). The expression of variety virulence factors may explain why T. pyogenes is able to cause such a diverse range of diseases. T. pyogenes strain 2012CQ-ZSH is Gram positive, nonmotile, nonsporulating, and polymorphic. In this study, strain 2012CQZSH was isolated from the infected goats from Chongqing, China, and its optimal temperature is 37°C. The genomic DNA of strain 2012CQ_ZSH was extracted using the DNeasy blood and tissue kit (Qiagen, Germany), according to the manufacturer’s protocol. The concentration and purity of DNA were measured by a NanoDrop spectrophotometer (ND1000; Thermo Fisher Scientific, DE). Genome sequencing of T. pyogenes strain 2012CQ-ZSH was performed at Sangon Biotech (Shanghai, China) employing the Illumina HiSeq 2500 sequencing platform. The clean data were used for assembly using Velvet 1.2.10 (3) and SPAdes 3.1.1 (4). The prediction of open reading frames (ORFs) was performed with Glimmer version 3.02 (5). Ribosomal RNAs were obtained by using RNAmmer version 1.2 (6), and tRNAs were identified by tRNAscan-SE version 1.21 (7). Then, the predicted genes were compared to NCBI nr, Swiss-Prot, Pfam, and COG databases. Meanwhile, we assigned translated amino acids into KEGG pathways using KEGG Automatic Annotation Server (KAAS) (8). SignalIP version 4.1 was used to identify genes with signal peptides, and THMMER 2.0 was performed to define genes with transmembrane helices (9). Clustered regularly interspaced short palindromic repeats (CRISPRs) were predicted by CRISPRfinder (10, 11). The genome sequence is 2,295,822 bp, with a G⫹C content 59.70%. The whole-genome sequence contains 2,019 predicted
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genes, 46 tRNAs, and six rRNAs. The genome encodes several virulence factors, including PLO, cbpA, nanH, nanP, fimC, and fimE. Moreover, genes regulating the formation of biofilms were also found in the genome sequence, such as luxS. The presence of the genome sequence of T. pyogenes may provide new approaches to develop antimicrobial drugs different from the traditional drugs, such as antipathogenic drugs which will not lead to resistant strains (12). In conclusion, the complete genome sequence of T. pyogenes will provide us new insights into its pathogenesis and virulence power. More importantly, the detailed information of the genome sequence offers a systematic approach for choosing vaccines and protecting local livestock from the infections. Accession number(s). This whole-genome shotgun project has been deposited in DDBJ/EMBL/GenBank under the GenBank accession no. CP012649. The version described in this paper is the first version, CP012649.1. ACKNOWLEDGMENTS This work was supported by National Natural Science Funds of China (grant no. 31402149) and basic and advanced research projects of Chongqing (cstc2015jcyjA80035).
FUNDING INFORMATION This work, including the efforts of Lizhi Fu, was funded by National Natural Science Funds of China. This work, including the efforts of Lizhi Fu, was funded by Basic and Advanced Projects of Chongqing.
REFERENCES 1. Nagib S, Rau J, Sammra O, Lämmler C, Schlez K, Zschöck M, PrengerBerninghoff E, Klein G, Abdulmawjood A. 2014. Identification of Trueperella pyogenes isolated from bovine mastitis by Fourier transform infrared spectroscopy. PLoS One 9:e104654. http://dx.doi.org/10.1371/ journal.pone.0104654. 2. Jost BH, Billington SJ. 2005. Arcanobacterium pyogenes: molecular pathogenesis of an animal opportunist. Antonie Van Leeuwenhoek 88:87–102. http://dx.doi.org/10.1007/s10482-005-2316-5. 3. Zerbino DR, Birney E. 2008. Velvet: algorithms for de novo short read
Genome Announcements
genomea.asm.org 1
Zhang et al.
4.
5. 6.
7.
assembly using de Bruijn graphs. Genome Res 18:821– 829. http:// dx.doi.org/10.1101/gr.074492.107. Bankevich A, Nurk S, Antipov D, Gurevich AA, Dvorkin M, Kulikov AS, Lesin VM, Nikolenko SI, Pham S, Prjibelski AD, Pyshkin AV, Sirotkin AV, Vyahhi N, Tesler G, Alekseyev MA, Pevzner PA. 2012. SPAdes: a new genome assembly algorithm and its applications to single-cell sequencing. J Comput Biol 19:455– 477. http://dx.doi.org/10.1089/cmb.2012.0021. Delcher AL, Bratke KA, Powers EC, Salzberg SL. 2007. Identifying bacterial genes and endosymbiont DNA with Glimmer. Bioinformatics 23:673– 679. http://dx.doi.org/10.1093/bioinformatics/btm009. Lagesen K, Hallin P, Rødland EA, Staerfeldt H-H, Rognes T, Ussery DW. 2007. RNAmmer: consistent and rapid annotation of ribosomal RNA genes. Nucleic Acids Res 35:3100 –3108. http://dx.doi.org/10.1093/ nar/gkm160. Lowe TM, Eddy SR. 1997. TRNAscan-SE: a program for improved detection of transfer RNA genes in genomic sequence. Nucleic Acids Res 25:955–964. http://dx.doi.org/10.1093/nar/25.5.0955.
2 genomea.asm.org
8. Moriya Y, Itoh M, Okuda S, Yoshizawa AC, Kanehisa M. 2007. KAAS: an automatic genome annotation and pathway reconstruction server. Nucleic Acids Res 35:W182–W185. http://dx.doi.org/10.1093/nar/gkm321. 9. Krogh A, Larsson B, von Heijne G, Sonnhammer EL. 2001. Predicting transmembrane protein topology with a hidden Markov model: application to complete genomes. J Mol Biol 305:567–580. http://dx.doi.org/ 10.1006/jmbi.2000.4315. 10. Grissa I, Vergnaud G, Pourcel C. 2007. CRISPRFinder: a Web tool to identify clustered regularly interspaced short palindromic repeats. Nucleic Acids Res 35:W52–W57. http://dx.doi.org/10.1093/nar/gkm360. 11. Grissa I, Vergnaud G, Pourcel C. 2007. The CRISPRdb database and tools to display CRISPRs and to generate dictionaries of spacers and repeats. BMC Bioinformatics 8:172. http://dx.doi.org/10.1186/1471-2105-8 -172. 12. Olson ME, Ceri H, Morck DW, Buret AG, Read RR. 2002. Biofilm bacteria: formation and comparative susceptibility to antibiotics. Can J Vet Res 66:86 –92.
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