Cargando…
Draft genome sequence of non-shiga toxin-producing Escherichia coli O157 NCCP15738
BACKGROUND: The non-shiga toxin-producing Escherichia coli (non-STEC) O157 is a pathogenic strain that cause diarrhea but does not cause hemolytic-uremic syndrome, or hemorrhagic colitis. Here, we present the 5-Mb draft genome sequence of non-STEC O157 NCCP15738, which was isolated from the feces of...
Autores principales: | , , , , , , |
---|---|
Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
BioMed Central
2016
|
Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4835932/ https://www.ncbi.nlm.nih.gov/pubmed/27096008 http://dx.doi.org/10.1186/s13099-016-0096-2 |
_version_ | 1782427696474619904 |
---|---|
author | Kwon, Taesoo Kim, Jung-Beom Bak, Young-Seok Yu, Young-Bin Kwon, Ki Sung Kim, Won Cho, Seung-Hak |
author_facet | Kwon, Taesoo Kim, Jung-Beom Bak, Young-Seok Yu, Young-Bin Kwon, Ki Sung Kim, Won Cho, Seung-Hak |
author_sort | Kwon, Taesoo |
collection | PubMed |
description | BACKGROUND: The non-shiga toxin-producing Escherichia coli (non-STEC) O157 is a pathogenic strain that cause diarrhea but does not cause hemolytic-uremic syndrome, or hemorrhagic colitis. Here, we present the 5-Mb draft genome sequence of non-STEC O157 NCCP15738, which was isolated from the feces of a Korean patient with diarrhea, and describe its features and the structural basis for its genome evolution. RESULTS: A total of 565-Mbp paired-end reads were generated using the Illumina-HiSeq 2000 platform. The reads were assembled into 135 scaffolds throughout the de novo assembly. The assembled genome size of NCCP15738 was 5,005,278 bp with an N50 value of 142,450 bp and 50.65 % G+C content. Using Rapid Annotation using Subsystem Technology analysis, we predicted 4780 ORFs and 31 RNA genes. The evolutionary tree was inferred from multiple sequence alignment of 45 E. coli species. The most closely related neighbor of NCCP15738 indicated by whole-genome phylogeny was E. coli UMNK88, but that indicated by multilocus sequence analysis was E. coli DH1(ME8569). CONCLUSIONS: A comparison between the NCCP15738 genome and those of reference strains, E. coli K-12 substr. MG1655 and EHEC O157:H7 EDL933 by bioinformatics analyses revealed unique genes in NCCP15738 associated with lysis protein S, two-component signal transduction system, conjugation, the flagellum, nucleotide-binding proteins, and metal-ion binding proteins. Notably, NCCP15738 has a dual flagella system like that in Vibrio parahaemolyticus, Aeromonas spp., and Rhodospirillum centenum. The draft genome sequence and the results of bioinformatics analysis of NCCP15738 provide the basis for understanding the genomic evolution of this strain. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1186/s13099-016-0096-2) contains supplementary material, which is available to authorized users. |
format | Online Article Text |
id | pubmed-4835932 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2016 |
publisher | BioMed Central |
record_format | MEDLINE/PubMed |
spelling | pubmed-48359322016-04-20 Draft genome sequence of non-shiga toxin-producing Escherichia coli O157 NCCP15738 Kwon, Taesoo Kim, Jung-Beom Bak, Young-Seok Yu, Young-Bin Kwon, Ki Sung Kim, Won Cho, Seung-Hak Gut Pathog Genome Report BACKGROUND: The non-shiga toxin-producing Escherichia coli (non-STEC) O157 is a pathogenic strain that cause diarrhea but does not cause hemolytic-uremic syndrome, or hemorrhagic colitis. Here, we present the 5-Mb draft genome sequence of non-STEC O157 NCCP15738, which was isolated from the feces of a Korean patient with diarrhea, and describe its features and the structural basis for its genome evolution. RESULTS: A total of 565-Mbp paired-end reads were generated using the Illumina-HiSeq 2000 platform. The reads were assembled into 135 scaffolds throughout the de novo assembly. The assembled genome size of NCCP15738 was 5,005,278 bp with an N50 value of 142,450 bp and 50.65 % G+C content. Using Rapid Annotation using Subsystem Technology analysis, we predicted 4780 ORFs and 31 RNA genes. The evolutionary tree was inferred from multiple sequence alignment of 45 E. coli species. The most closely related neighbor of NCCP15738 indicated by whole-genome phylogeny was E. coli UMNK88, but that indicated by multilocus sequence analysis was E. coli DH1(ME8569). CONCLUSIONS: A comparison between the NCCP15738 genome and those of reference strains, E. coli K-12 substr. MG1655 and EHEC O157:H7 EDL933 by bioinformatics analyses revealed unique genes in NCCP15738 associated with lysis protein S, two-component signal transduction system, conjugation, the flagellum, nucleotide-binding proteins, and metal-ion binding proteins. Notably, NCCP15738 has a dual flagella system like that in Vibrio parahaemolyticus, Aeromonas spp., and Rhodospirillum centenum. The draft genome sequence and the results of bioinformatics analysis of NCCP15738 provide the basis for understanding the genomic evolution of this strain. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1186/s13099-016-0096-2) contains supplementary material, which is available to authorized users. BioMed Central 2016-04-19 /pmc/articles/PMC4835932/ /pubmed/27096008 http://dx.doi.org/10.1186/s13099-016-0096-2 Text en © Kwon et al. 2016 Open AccessThis article is distributed under the terms of the Creative Commons Attribution 4.0 International License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated. |
spellingShingle | Genome Report Kwon, Taesoo Kim, Jung-Beom Bak, Young-Seok Yu, Young-Bin Kwon, Ki Sung Kim, Won Cho, Seung-Hak Draft genome sequence of non-shiga toxin-producing Escherichia coli O157 NCCP15738 |
title | Draft genome sequence of non-shiga toxin-producing Escherichia coli O157 NCCP15738 |
title_full | Draft genome sequence of non-shiga toxin-producing Escherichia coli O157 NCCP15738 |
title_fullStr | Draft genome sequence of non-shiga toxin-producing Escherichia coli O157 NCCP15738 |
title_full_unstemmed | Draft genome sequence of non-shiga toxin-producing Escherichia coli O157 NCCP15738 |
title_short | Draft genome sequence of non-shiga toxin-producing Escherichia coli O157 NCCP15738 |
title_sort | draft genome sequence of non-shiga toxin-producing escherichia coli o157 nccp15738 |
topic | Genome Report |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4835932/ https://www.ncbi.nlm.nih.gov/pubmed/27096008 http://dx.doi.org/10.1186/s13099-016-0096-2 |
work_keys_str_mv | AT kwontaesoo draftgenomesequenceofnonshigatoxinproducingescherichiacolio157nccp15738 AT kimjungbeom draftgenomesequenceofnonshigatoxinproducingescherichiacolio157nccp15738 AT bakyoungseok draftgenomesequenceofnonshigatoxinproducingescherichiacolio157nccp15738 AT yuyoungbin draftgenomesequenceofnonshigatoxinproducingescherichiacolio157nccp15738 AT kwonkisung draftgenomesequenceofnonshigatoxinproducingescherichiacolio157nccp15738 AT kimwon draftgenomesequenceofnonshigatoxinproducingescherichiacolio157nccp15738 AT choseunghak draftgenomesequenceofnonshigatoxinproducingescherichiacolio157nccp15738 |