[KSCI] Korea Science Citation Index Service

http://dx.doi.org/10.5187/jast.2021.e38

Complete genome sequence of Escherichia coli K_EC180, a bacterium producing shiga-like toxin isolated from swine feces

Kim, Hyeri (Department of Animal Resources Science, Dankook University)
Cho, Jae Hyoung (Department of Animal Resources Science, Dankook University)
Cho, Jin Ho (Division of Food and Animal Science, Chungbuk National University)
Song, Minho (Division of Animal and Dairy Science, Chungnam National University)
Shin, Hakdong (Department of Food Science and Biotechnology, College of Life Science, Sejong University)
Kim, Sheena (Department of Animal Resources Science, Dankook University)
Kim, Eun Sol (Department of Animal Resources Science, Dankook University)
Kim, Hyeun Bum (Department of Animal Resources Science, Dankook University)
Lee, Ju-Hoon (Department of Food Animal Biotechnology, Department of Agricultural Biotechnology, Center for Food and Bioconvergence, Seoul National University)

Publication Information

Journal of Animal Science and Technology / v.63, no.2, 2021 , pp. 461-464 More about this Journal

Abstract

Escherichia coli normally colonizes the lower intestine of animals and humans, but some serotypes are foodborne pathogens. The Escherichia coli K_EC180 was isolated from swine feces that were collected from a weaner pig. In this genome announcement, E. coli K_EC180 was sequenced using PacBio RS II and Illumina NextSeq 500 platforms. The complete chromosome of E. coli K_EC180 is composed of one circular chromosome (5,017,281 bp) with 50.4% of guanine + cytosine (G + C) content, 4,935 of coding sequence (CDS), 88 of tRNA, and 22 of rRNA genes. The complete genome of E. coli K_EC180 contains the toxin genes such as shiga-like toxins (stxA and stxB).

Keywords

Escherichia coli K_EC180; Swine feces; Whole genome sequencing; Shiga-like toxin;

Citations & Related Records

Reference

1	Guevarra RB, Lee JH, Lee SH, Seok MJ, Kim DW, Kang BN, et al. Piglet gut microbial shifts early in life: causes and effects. J Anim Sci Biotechnol. 2019;10:1. https://doi.org/10.1186/s40104-018-0308-3 DOI
2	Li H. Aligning sequence reads, clone sequences and assembly contigs with BWA-MEM. arXiv. https://arxiv.org/abs/1303.3997
3	Walker BJ, Abeel T, Shea T, Priest M, Abouelliel A, Sakthikumar S, et al. Pilon: an integrated tool for comprehensive microbial variant detection and genome assembly improvement. PLOS ONE. 2014;9:e112963. https://doi.org/10.1371/journal.pone.0112963 DOI
4	Simao FA, Waterhouse RM, Ioannidis P, Kriventseva EV, Zdobnov EM. BUSCO: assessing genome assembly and annotation completeness with single-copy orthologs. Bioinformatics. 2015;31:3210-2. https://doi.org/10.1093/bioinformatics/btv351 DOI
5	Gurevich A, Saveliev V, Vyahhi N, Tesler G. QUAST: quality assessment tool for genome assemblies. Bioinformatics. 2013;29:1072-5. https://doi.org/10.1093/bioinformatics/btt086 DOI
6	Seemann T. Prokka: rapid prokaryotic genome annotation. Bioinformatics. 2014;30:2068-9. https://doi.org/10.1093/bioinformatics/btu153 DOI
7	Aziz RK, Bartels D, Best AA, DeJongh M, Disz T, Edwards RA, et al. The RAST server: rapid annotations using subsystems technology. BMC Genomics. 2008;9:75. https://doi.org/10.1186/1471-2164-9-75 DOI
8	Liu B, Zheng D, Jin Q, Chen L, Yang J. VFDB 2019: a comparative pathogenomic platform with an interactive web interface. Nucl Acids Res. 2019;47:D687-92. DOI
9	Tesh VL, O'Brien AD. The pathogenic mechanisms of Shiga toxin and the Shiga-like toxins. Mol Microbiol. 1991;5:1817-22. https://doi.org/10.1111/j.1365-2958.1991.tb00805.x DOI
10	O'Brien AD, Holmes RK. Shiga and Shiga-like toxins. Microbiol Rev. 1987;51:206-20. https://doi.org/10.1128/MR.51.2.206-220.1987 DOI