Sequencing and validation of the genome of a Campylobacter concisus reveals intra-species diversity.

Campylobacter concisus is an emerging pathogen of the human gastrointestinal tract. Its role in different diseases remains a subject of debate; this may be due to strain to strain genetic variation. Here, we sequence and analyze the genome of a C. concisus from a biopsy of a child with Crohn's...

Descripción completa

Guardado en:

Detalles Bibliográficos
Autores principales:	Nandan P Deshpande, Nadeem O Kaakoush, Hazel Mitchell, Karolina Janitz, Mark J Raftery, Simone S Li, Marc R Wilkins
Formato:	article
Lenguaje:	EN
Publicado:	Public Library of Science (PLoS) 2011
Materias:	Medicine R Science Q
Acceso en línea:	https://doaj.org/article/c03d77a5c6774eadbf5fa9d0112209ed
Etiquetas:	Agregar Etiqueta Sin Etiquetas, Sea el primero en etiquetar este registro!

id	oai:doaj.org-article:c03d77a5c6774eadbf5fa9d0112209ed
record_format	dspace
spelling	oai:doaj.org-article:c03d77a5c6774eadbf5fa9d0112209ed2021-11-18T06:49:04ZSequencing and validation of the genome of a Campylobacter concisus reveals intra-species diversity.1932-620310.1371/journal.pone.0022170https://doaj.org/article/c03d77a5c6774eadbf5fa9d0112209ed2011-01-01T00:00:00Zhttps://www.ncbi.nlm.nih.gov/pmc/articles/pmid/21829448/pdf/?tool=EBIhttps://doaj.org/toc/1932-6203Campylobacter concisus is an emerging pathogen of the human gastrointestinal tract. Its role in different diseases remains a subject of debate; this may be due to strain to strain genetic variation. Here, we sequence and analyze the genome of a C. concisus from a biopsy of a child with Crohn's disease (UNSWCD); the second such genome for this species. A 1.8 Mb genome was assembled with paired-end reads from a next-generation sequencer. This genome is smaller than the 2.1 Mb C. concisus reference BAA-1457. While 1593 genes were conserved across UNSWCD and BAA-1457, 138 genes from UNSWCD and 281 from BAA-1457 were unique when compared against the other. To further validate the genome assembly and annotation, comprehensive shotgun proteomics was performed. This confirmed 78% of open reading frames in UNSWCD and, importantly, provided evidence of expression for 217 proteins previously defined as 'hypothetical' in Campylobacter. Substantial functional differences were observed between the UNSWCD and the reference strain. Enrichment analysis revealed differences in membrane proteins, response to stimulus, molecular transport and electron carriers. Synteny maps for the 281 genes not present in UNSWCD identified seven functionally associated gene clusters. These included one associated with the CRISPR family and another which encoded multiple restriction endonucleases; these genes are all involved in resistance to phage attack. Many of the observed differences are consistent with UNSWCD having adapted to greater surface interaction with host cells, as opposed to BAA-1457 which may prefer a free-living environment.Nandan P DeshpandeNadeem O KaakoushHazel MitchellKarolina JanitzMark J RafterySimone S LiMarc R WilkinsPublic Library of Science (PLoS)articleMedicineRScienceQENPLoS ONE, Vol 6, Iss 7, p e22170 (2011)
institution	DOAJ
collection	DOAJ
language	EN
topic	Medicine R Science Q
spellingShingle	Medicine R Science Q Nandan P Deshpande Nadeem O Kaakoush Hazel Mitchell Karolina Janitz Mark J Raftery Simone S Li Marc R Wilkins Sequencing and validation of the genome of a Campylobacter concisus reveals intra-species diversity.
description	Campylobacter concisus is an emerging pathogen of the human gastrointestinal tract. Its role in different diseases remains a subject of debate; this may be due to strain to strain genetic variation. Here, we sequence and analyze the genome of a C. concisus from a biopsy of a child with Crohn's disease (UNSWCD); the second such genome for this species. A 1.8 Mb genome was assembled with paired-end reads from a next-generation sequencer. This genome is smaller than the 2.1 Mb C. concisus reference BAA-1457. While 1593 genes were conserved across UNSWCD and BAA-1457, 138 genes from UNSWCD and 281 from BAA-1457 were unique when compared against the other. To further validate the genome assembly and annotation, comprehensive shotgun proteomics was performed. This confirmed 78% of open reading frames in UNSWCD and, importantly, provided evidence of expression for 217 proteins previously defined as 'hypothetical' in Campylobacter. Substantial functional differences were observed between the UNSWCD and the reference strain. Enrichment analysis revealed differences in membrane proteins, response to stimulus, molecular transport and electron carriers. Synteny maps for the 281 genes not present in UNSWCD identified seven functionally associated gene clusters. These included one associated with the CRISPR family and another which encoded multiple restriction endonucleases; these genes are all involved in resistance to phage attack. Many of the observed differences are consistent with UNSWCD having adapted to greater surface interaction with host cells, as opposed to BAA-1457 which may prefer a free-living environment.
format	article
author	Nandan P Deshpande Nadeem O Kaakoush Hazel Mitchell Karolina Janitz Mark J Raftery Simone S Li Marc R Wilkins
author_facet	Nandan P Deshpande Nadeem O Kaakoush Hazel Mitchell Karolina Janitz Mark J Raftery Simone S Li Marc R Wilkins
author_sort	Nandan P Deshpande
title	Sequencing and validation of the genome of a Campylobacter concisus reveals intra-species diversity.
title_short	Sequencing and validation of the genome of a Campylobacter concisus reveals intra-species diversity.
title_full	Sequencing and validation of the genome of a Campylobacter concisus reveals intra-species diversity.
title_fullStr	Sequencing and validation of the genome of a Campylobacter concisus reveals intra-species diversity.
title_full_unstemmed	Sequencing and validation of the genome of a Campylobacter concisus reveals intra-species diversity.
title_sort	sequencing and validation of the genome of a campylobacter concisus reveals intra-species diversity.
publisher	Public Library of Science (PLoS)
publishDate	2011
url	https://doaj.org/article/c03d77a5c6774eadbf5fa9d0112209ed
work_keys_str_mv	AT nandanpdeshpande sequencingandvalidationofthegenomeofacampylobacterconcisusrevealsintraspeciesdiversity AT nadeemokaakoush sequencingandvalidationofthegenomeofacampylobacterconcisusrevealsintraspeciesdiversity AT hazelmitchell sequencingandvalidationofthegenomeofacampylobacterconcisusrevealsintraspeciesdiversity AT karolinajanitz sequencingandvalidationofthegenomeofacampylobacterconcisusrevealsintraspeciesdiversity AT markjraftery sequencingandvalidationofthegenomeofacampylobacterconcisusrevealsintraspeciesdiversity AT simonesli sequencingandvalidationofthegenomeofacampylobacterconcisusrevealsintraspeciesdiversity AT marcrwilkins sequencingandvalidationofthegenomeofacampylobacterconcisusrevealsintraspeciesdiversity
_version_	1718424376839241728

Sequencing and validation of the genome of a Campylobacter concisus reveals intra-species diversity.

Ejemplares similares