Functional annotation and distribution overview of RNA families in 27 Streptococcus agalactiae genomes

Autores
Wolf, Ivan Rodrigo; Paschoal, Alexandre Rossi; Quiroga, Cecilia; Domingues, Douglas Silva; de Souza, Rogério Fernandes; Pretto Giordano, Lucienne Garcia; Vilas Boas, Laurival Antonio
Año de publicación
2018
Idioma
inglés
Tipo de recurso
artículo
Estado
versión publicada
Descripción
Background: Streptococcus agalactiae, also known as Group B Streptococcus (GBS), is a Gram-positive bacterium that colonizes the gastrointestinal and genitourinary tract of humans. This bacterium has also been isolated from various animals, such as fish and cattle. Non-coding RNAs (ncRNAs) can act as regulators of gene expression in bacteria, such as Streptococcus pneumoniae and Streptococcus pyogenes. However, little is known about the genomic distribution of ncRNAs and RNA families in S. agalactiae. Results: Comparative genome analysis of 27 S. agalactiae strains showed more than 5 thousand genomic regions identified and classified as Core, Exclusive, and Shared genome sequences. We identified 27 to 89 RNA families per genome distributed over these regions, from these, 25 were in Core regions while Shared and Exclusive regions showed variations amongst strains. We propose that the amount and type of ncRNA present in each genome can provide a pattern to contribute in the identification of the clonal types. Conclusions: The identification of RNA families provides an insight over ncRNAs, sRNAs and ribozymes function, that can be further explored as targets for antibiotic development or studied in gene regulation of cellular processes. RNA families could be considered as markers to determine infection capabilities of different strains. Lastly, pan-genome analysis of GBS including the full range of functional transcripts provides a broader approach in the understanding of this pathogen.
Fil: Wolf, Ivan Rodrigo. Universidade Estadual de Londrina; Brasil
Fil: Paschoal, Alexandre Rossi. Universidade Federal do Paraná; Brasil
Fil: Quiroga, Cecilia. Consejo Nacional de Investigaciones Científicas y Técnicas. Oficina de Coordinación Administrativa Houssay. Instituto de Investigaciones en Microbiología y Parasitología Médica. Universidad de Buenos Aires. Facultad de Medicina. Instituto de Investigaciones en Microbiología y Parasitología Médica; Argentina
Fil: Domingues, Douglas Silva. Universidade Estadual Paulista Julio de Mesquita Filho; Brasil
Fil: de Souza, Rogério Fernandes. Universidade Estadual de Londrina; Brasil
Fil: Pretto Giordano, Lucienne Garcia. Universidade Estadual de Londrina; Brasil
Fil: Vilas Boas, Laurival Antonio. Universidade Estadual de Londrina; Brasil
Materia
STREPTOCOCCUS
NON-CODING RNAS
PAN-GENOME
RNA FAMILIES
TRANSCRIPTOME
Nivel de accesibilidad
acceso abierto
Condiciones de uso
https://creativecommons.org/licenses/by-nc-sa/2.5/ar/
Repositorio
CONICET Digital (CONICET)
Institución
Consejo Nacional de Investigaciones Científicas y Técnicas
OAI Identificador
oai:ri.conicet.gov.ar:11336/86968
Acceder
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oai_identifier_str oai:ri.conicet.gov.ar:11336/86968
network_acronym_str CONICETDig
repository_id_str 3498
network_name_str CONICET Digital (CONICET)
spelling Functional annotation and distribution overview of RNA families in 27 Streptococcus agalactiae genomesWolf, Ivan RodrigoPaschoal, Alexandre RossiQuiroga, CeciliaDomingues, Douglas Silvade Souza, Rogério FernandesPretto Giordano, Lucienne GarciaVilas Boas, Laurival AntonioSTREPTOCOCCUSNON-CODING RNASPAN-GENOMERNA FAMILIESTRANSCRIPTOMEhttps://purl.org/becyt/ford/1.6https://purl.org/becyt/ford/1Background: Streptococcus agalactiae, also known as Group B Streptococcus (GBS), is a Gram-positive bacterium that colonizes the gastrointestinal and genitourinary tract of humans. This bacterium has also been isolated from various animals, such as fish and cattle. Non-coding RNAs (ncRNAs) can act as regulators of gene expression in bacteria, such as Streptococcus pneumoniae and Streptococcus pyogenes. However, little is known about the genomic distribution of ncRNAs and RNA families in S. agalactiae. Results: Comparative genome analysis of 27 S. agalactiae strains showed more than 5 thousand genomic regions identified and classified as Core, Exclusive, and Shared genome sequences. We identified 27 to 89 RNA families per genome distributed over these regions, from these, 25 were in Core regions while Shared and Exclusive regions showed variations amongst strains. We propose that the amount and type of ncRNA present in each genome can provide a pattern to contribute in the identification of the clonal types. Conclusions: The identification of RNA families provides an insight over ncRNAs, sRNAs and ribozymes function, that can be further explored as targets for antibiotic development or studied in gene regulation of cellular processes. RNA families could be considered as markers to determine infection capabilities of different strains. Lastly, pan-genome analysis of GBS including the full range of functional transcripts provides a broader approach in the understanding of this pathogen.Fil: Wolf, Ivan Rodrigo. Universidade Estadual de Londrina; BrasilFil: Paschoal, Alexandre Rossi. Universidade Federal do Paraná; BrasilFil: Quiroga, Cecilia. Consejo Nacional de Investigaciones Científicas y Técnicas. Oficina de Coordinación Administrativa Houssay. Instituto de Investigaciones en Microbiología y Parasitología Médica. Universidad de Buenos Aires. Facultad de Medicina. Instituto de Investigaciones en Microbiología y Parasitología Médica; ArgentinaFil: Domingues, Douglas Silva. Universidade Estadual Paulista Julio de Mesquita Filho; BrasilFil: de Souza, Rogério Fernandes. Universidade Estadual de Londrina; BrasilFil: Pretto Giordano, Lucienne Garcia. Universidade Estadual de Londrina; BrasilFil: Vilas Boas, Laurival Antonio. Universidade Estadual de Londrina; BrasilBioMed Central2018-07info:eu-repo/semantics/articleinfo:eu-repo/semantics/publishedVersionhttp://purl.org/coar/resource_type/c_6501info:ar-repo/semantics/articuloapplication/pdfapplication/vnd.openxmlformats-officedocument.wordprocessingml.documentapplication/pdfhttp://hdl.handle.net/11336/86968Wolf, Ivan Rodrigo; Paschoal, Alexandre Rossi; Quiroga, Cecilia; Domingues, Douglas Silva; de Souza, Rogério Fernandes; et al.; Functional annotation and distribution overview of RNA families in 27 Streptococcus agalactiae genomes; BioMed Central; BMC Genomics; 19; 556; 7-2018; 1-111471-21641471-2164CONICET DigitalCONICETenginfo:eu-repo/semantics/altIdentifier/url/https://bmcgenomics.biomedcentral.com/articles/10.1186/s12864-018-4951-zinfo:eu-repo/semantics/altIdentifier/doi/10.1186/s12864-018-4951-zinfo:eu-repo/semantics/openAccesshttps://creativecommons.org/licenses/by-nc-sa/2.5/ar/reponame:CONICET Digital (CONICET)instname:Consejo Nacional de Investigaciones Científicas y Técnicas2025-09-03T10:05:09Zoai:ri.conicet.gov.ar:11336/86968instacron:CONICETInstitucionalhttp://ri.conicet.gov.ar/Organismo científico-tecnológicoNo correspondehttp://ri.conicet.gov.ar/oai/requestdasensio@conicet.gov.ar; lcarlino@conicet.gov.arArgentinaNo correspondeNo correspondeNo correspondeopendoar:34982025-09-03 10:05:10.263CONICET Digital (CONICET) - Consejo Nacional de Investigaciones Científicas y Técnicasfalse
dc.title.none.fl_str_mv Functional annotation and distribution overview of RNA families in 27 Streptococcus agalactiae genomes
title Functional annotation and distribution overview of RNA families in 27 Streptococcus agalactiae genomes
spellingShingle Functional annotation and distribution overview of RNA families in 27 Streptococcus agalactiae genomes
Wolf, Ivan Rodrigo
STREPTOCOCCUS
NON-CODING RNAS
PAN-GENOME
RNA FAMILIES
TRANSCRIPTOME
title_short Functional annotation and distribution overview of RNA families in 27 Streptococcus agalactiae genomes
title_full Functional annotation and distribution overview of RNA families in 27 Streptococcus agalactiae genomes
title_fullStr Functional annotation and distribution overview of RNA families in 27 Streptococcus agalactiae genomes
title_full_unstemmed Functional annotation and distribution overview of RNA families in 27 Streptococcus agalactiae genomes
title_sort Functional annotation and distribution overview of RNA families in 27 Streptococcus agalactiae genomes
dc.creator.none.fl_str_mv Wolf, Ivan Rodrigo
Paschoal, Alexandre Rossi
Quiroga, Cecilia
Domingues, Douglas Silva
de Souza, Rogério Fernandes
Pretto Giordano, Lucienne Garcia
Vilas Boas, Laurival Antonio
author Wolf, Ivan Rodrigo
author_facet Wolf, Ivan Rodrigo
Paschoal, Alexandre Rossi
Quiroga, Cecilia
Domingues, Douglas Silva
de Souza, Rogério Fernandes
Pretto Giordano, Lucienne Garcia
Vilas Boas, Laurival Antonio
author_role author
author2 Paschoal, Alexandre Rossi
Quiroga, Cecilia
Domingues, Douglas Silva
de Souza, Rogério Fernandes
Pretto Giordano, Lucienne Garcia
Vilas Boas, Laurival Antonio
author2_role author
author
author
author
author
author
dc.subject.none.fl_str_mv STREPTOCOCCUS
NON-CODING RNAS
PAN-GENOME
RNA FAMILIES
TRANSCRIPTOME
topic STREPTOCOCCUS
NON-CODING RNAS
PAN-GENOME
RNA FAMILIES
TRANSCRIPTOME
purl_subject.fl_str_mv https://purl.org/becyt/ford/1.6
https://purl.org/becyt/ford/1
dc.description.none.fl_txt_mv Background: Streptococcus agalactiae, also known as Group B Streptococcus (GBS), is a Gram-positive bacterium that colonizes the gastrointestinal and genitourinary tract of humans. This bacterium has also been isolated from various animals, such as fish and cattle. Non-coding RNAs (ncRNAs) can act as regulators of gene expression in bacteria, such as Streptococcus pneumoniae and Streptococcus pyogenes. However, little is known about the genomic distribution of ncRNAs and RNA families in S. agalactiae. Results: Comparative genome analysis of 27 S. agalactiae strains showed more than 5 thousand genomic regions identified and classified as Core, Exclusive, and Shared genome sequences. We identified 27 to 89 RNA families per genome distributed over these regions, from these, 25 were in Core regions while Shared and Exclusive regions showed variations amongst strains. We propose that the amount and type of ncRNA present in each genome can provide a pattern to contribute in the identification of the clonal types. Conclusions: The identification of RNA families provides an insight over ncRNAs, sRNAs and ribozymes function, that can be further explored as targets for antibiotic development or studied in gene regulation of cellular processes. RNA families could be considered as markers to determine infection capabilities of different strains. Lastly, pan-genome analysis of GBS including the full range of functional transcripts provides a broader approach in the understanding of this pathogen.
Fil: Wolf, Ivan Rodrigo. Universidade Estadual de Londrina; Brasil
Fil: Paschoal, Alexandre Rossi. Universidade Federal do Paraná; Brasil
Fil: Quiroga, Cecilia. Consejo Nacional de Investigaciones Científicas y Técnicas. Oficina de Coordinación Administrativa Houssay. Instituto de Investigaciones en Microbiología y Parasitología Médica. Universidad de Buenos Aires. Facultad de Medicina. Instituto de Investigaciones en Microbiología y Parasitología Médica; Argentina
Fil: Domingues, Douglas Silva. Universidade Estadual Paulista Julio de Mesquita Filho; Brasil
Fil: de Souza, Rogério Fernandes. Universidade Estadual de Londrina; Brasil
Fil: Pretto Giordano, Lucienne Garcia. Universidade Estadual de Londrina; Brasil
Fil: Vilas Boas, Laurival Antonio. Universidade Estadual de Londrina; Brasil
description Background: Streptococcus agalactiae, also known as Group B Streptococcus (GBS), is a Gram-positive bacterium that colonizes the gastrointestinal and genitourinary tract of humans. This bacterium has also been isolated from various animals, such as fish and cattle. Non-coding RNAs (ncRNAs) can act as regulators of gene expression in bacteria, such as Streptococcus pneumoniae and Streptococcus pyogenes. However, little is known about the genomic distribution of ncRNAs and RNA families in S. agalactiae. Results: Comparative genome analysis of 27 S. agalactiae strains showed more than 5 thousand genomic regions identified and classified as Core, Exclusive, and Shared genome sequences. We identified 27 to 89 RNA families per genome distributed over these regions, from these, 25 were in Core regions while Shared and Exclusive regions showed variations amongst strains. We propose that the amount and type of ncRNA present in each genome can provide a pattern to contribute in the identification of the clonal types. Conclusions: The identification of RNA families provides an insight over ncRNAs, sRNAs and ribozymes function, that can be further explored as targets for antibiotic development or studied in gene regulation of cellular processes. RNA families could be considered as markers to determine infection capabilities of different strains. Lastly, pan-genome analysis of GBS including the full range of functional transcripts provides a broader approach in the understanding of this pathogen.
publishDate 2018
dc.date.none.fl_str_mv 2018-07
dc.type.none.fl_str_mv info:eu-repo/semantics/article
info:eu-repo/semantics/publishedVersion
http://purl.org/coar/resource_type/c_6501
info:ar-repo/semantics/articulo
format article
status_str publishedVersion
dc.identifier.none.fl_str_mv http://hdl.handle.net/11336/86968
Wolf, Ivan Rodrigo; Paschoal, Alexandre Rossi; Quiroga, Cecilia; Domingues, Douglas Silva; de Souza, Rogério Fernandes; et al.; Functional annotation and distribution overview of RNA families in 27 Streptococcus agalactiae genomes; BioMed Central; BMC Genomics; 19; 556; 7-2018; 1-11
1471-2164
1471-2164
CONICET Digital
CONICET
url http://hdl.handle.net/11336/86968
identifier_str_mv Wolf, Ivan Rodrigo; Paschoal, Alexandre Rossi; Quiroga, Cecilia; Domingues, Douglas Silva; de Souza, Rogério Fernandes; et al.; Functional annotation and distribution overview of RNA families in 27 Streptococcus agalactiae genomes; BioMed Central; BMC Genomics; 19; 556; 7-2018; 1-11
1471-2164
CONICET Digital
CONICET
dc.language.none.fl_str_mv eng
language eng
dc.relation.none.fl_str_mv info:eu-repo/semantics/altIdentifier/url/https://bmcgenomics.biomedcentral.com/articles/10.1186/s12864-018-4951-z
info:eu-repo/semantics/altIdentifier/doi/10.1186/s12864-018-4951-z
dc.rights.none.fl_str_mv info:eu-repo/semantics/openAccess
https://creativecommons.org/licenses/by-nc-sa/2.5/ar/
eu_rights_str_mv openAccess
rights_invalid_str_mv https://creativecommons.org/licenses/by-nc-sa/2.5/ar/
dc.format.none.fl_str_mv application/pdf
application/vnd.openxmlformats-officedocument.wordprocessingml.document
application/pdf
dc.publisher.none.fl_str_mv BioMed Central
publisher.none.fl_str_mv BioMed Central
dc.source.none.fl_str_mv reponame:CONICET Digital (CONICET)
instname:Consejo Nacional de Investigaciones Científicas y Técnicas
reponame_str CONICET Digital (CONICET)
collection CONICET Digital (CONICET)
instname_str Consejo Nacional de Investigaciones Científicas y Técnicas
repository.name.fl_str_mv CONICET Digital (CONICET) - Consejo Nacional de Investigaciones Científicas y Técnicas
repository.mail.fl_str_mv dasensio@conicet.gov.ar; lcarlino@conicet.gov.ar
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score 13.13397

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