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Draft genome sequence of non-shiga toxin-producing Escherichia coli O157 NCCP15738.

Kwon T, Kim JB, Bak YS, Yu YB, Kwon KS, Kim W, Cho SH - Gut Pathog (2016)

Bottom Line: 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.

View Article: PubMed Central - PubMed

Affiliation: School of Biological Sciences, Seoul National University, 1 Gwanak-ro, Gwanak-gu, Seoul, 151-742 Republic of Korea ; Division of Biosafety Evaluation and Control, Korea National Institute of Health, Cheongju, 363-951 Republic of Korea.

ABSTRACT

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.

No MeSH data available.


Related in: MedlinePlus

Subsystem category distribution of NCCP15738 based on SEED databases
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Fig1: Subsystem category distribution of NCCP15738 based on SEED databases

Mentions: Whole-genome sequencing by Illumina-HiSeq 2000 showed 565,810,000 bp with paired end reads that were 90 bp in length. After quality control, 504 Mbp of high quality reads were kept for assembly. The average sequencing depth was 86.7-fold coverage and the coverage ratio was 84.77 %. The high quality reads were assembled into 135 scaffolds by de novo assembly with an N50 value of 142,450 bp. The predicted genome size of NCCP15738 was 5,005,278 bp with 50.65 % G+C content. RAST analysis identified 4780 putative ORFs and 31 RNA genes, of which 4181 (80.6 %) could be functionally annotated (Fig. 1). The monosaccharides (212 ORFs) and central carbohydrate metabolism (135 ORFs) subsystems were significantly abundant among the subsystems (18.7 %). According to the subsystem results, we can assume that the NCCP15738 developed systems that can utilize various monosaccharides in addition to glucose to adapt to an extreme environment. A large number of ORFs were also associated with the “Amino acids and derivatives” subsystem (395 ORFs), “cofactors, vitamins, prosthetic groups, pigments” subsystem (266 ORFs) and “cell wall and capsule” subsystem (266 ORFs).Fig. 1


Draft genome sequence of non-shiga toxin-producing Escherichia coli O157 NCCP15738.

Kwon T, Kim JB, Bak YS, Yu YB, Kwon KS, Kim W, Cho SH - Gut Pathog (2016)

Subsystem category distribution of NCCP15738 based on SEED databases
© Copyright Policy - OpenAccess
Related In: Results  -  Collection

License 1 - License 2
Show All Figures
getmorefigures.php?uid=PMC4835932&req=5

Fig1: Subsystem category distribution of NCCP15738 based on SEED databases
Mentions: Whole-genome sequencing by Illumina-HiSeq 2000 showed 565,810,000 bp with paired end reads that were 90 bp in length. After quality control, 504 Mbp of high quality reads were kept for assembly. The average sequencing depth was 86.7-fold coverage and the coverage ratio was 84.77 %. The high quality reads were assembled into 135 scaffolds by de novo assembly with an N50 value of 142,450 bp. The predicted genome size of NCCP15738 was 5,005,278 bp with 50.65 % G+C content. RAST analysis identified 4780 putative ORFs and 31 RNA genes, of which 4181 (80.6 %) could be functionally annotated (Fig. 1). The monosaccharides (212 ORFs) and central carbohydrate metabolism (135 ORFs) subsystems were significantly abundant among the subsystems (18.7 %). According to the subsystem results, we can assume that the NCCP15738 developed systems that can utilize various monosaccharides in addition to glucose to adapt to an extreme environment. A large number of ORFs were also associated with the “Amino acids and derivatives” subsystem (395 ORFs), “cofactors, vitamins, prosthetic groups, pigments” subsystem (266 ORFs) and “cell wall and capsule” subsystem (266 ORFs).Fig. 1

Bottom Line: 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.

View Article: PubMed Central - PubMed

Affiliation: School of Biological Sciences, Seoul National University, 1 Gwanak-ro, Gwanak-gu, Seoul, 151-742 Republic of Korea ; Division of Biosafety Evaluation and Control, Korea National Institute of Health, Cheongju, 363-951 Republic of Korea.

ABSTRACT

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.

No MeSH data available.


Related in: MedlinePlus