Pan-Genome of the Genus Streptomyces and Prioritization of Biosynthetic Gene Clusters With Potential to Produce Antibiotic Compounds
ABSTRACT: Species of the genus Streptomyces are known for their ability to produce multiple secondary metabolites; their genomes have been extensively explored to discover new bioactive compounds. The richness of genomic data currently available allows filtering for high quality genomes, which in tu...
- Autores:
-
Caicedo Montoya, Carlos
Manzo Ruiz, Monserrat
Ríos Estepa, Rigoberto
- Tipo de recurso:
- Article of investigation
- Fecha de publicación:
- 2021
- Institución:
- Universidad de Antioquia
- Repositorio:
- Repositorio UdeA
- Idioma:
- eng
- OAI Identifier:
- oai:bibliotecadigital.udea.edu.co:10495/23813
- Acceso en línea:
- http://hdl.handle.net/10495/23813
- Palabra clave:
- Streptomyces
Genoma
Genome
Compuestos bioactivos
Bioactive compounds
Pan-genome
Genome mining
Biosynthetic gene cluster
Pangenoma
http://aims.fao.org/aos/agrovoc/c_ec4deb8c
- Rights
- openAccess
- License
- https://creativecommons.org/licenses/by/2.5/co/
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|
dc.title.spa.fl_str_mv |
Pan-Genome of the Genus Streptomyces and Prioritization of Biosynthetic Gene Clusters With Potential to Produce Antibiotic Compounds |
title |
Pan-Genome of the Genus Streptomyces and Prioritization of Biosynthetic Gene Clusters With Potential to Produce Antibiotic Compounds |
spellingShingle |
Pan-Genome of the Genus Streptomyces and Prioritization of Biosynthetic Gene Clusters With Potential to Produce Antibiotic Compounds Streptomyces Genoma Genome Compuestos bioactivos Bioactive compounds Pan-genome Genome mining Biosynthetic gene cluster Pangenoma http://aims.fao.org/aos/agrovoc/c_ec4deb8c |
title_short |
Pan-Genome of the Genus Streptomyces and Prioritization of Biosynthetic Gene Clusters With Potential to Produce Antibiotic Compounds |
title_full |
Pan-Genome of the Genus Streptomyces and Prioritization of Biosynthetic Gene Clusters With Potential to Produce Antibiotic Compounds |
title_fullStr |
Pan-Genome of the Genus Streptomyces and Prioritization of Biosynthetic Gene Clusters With Potential to Produce Antibiotic Compounds |
title_full_unstemmed |
Pan-Genome of the Genus Streptomyces and Prioritization of Biosynthetic Gene Clusters With Potential to Produce Antibiotic Compounds |
title_sort |
Pan-Genome of the Genus Streptomyces and Prioritization of Biosynthetic Gene Clusters With Potential to Produce Antibiotic Compounds |
dc.creator.fl_str_mv |
Caicedo Montoya, Carlos Manzo Ruiz, Monserrat Ríos Estepa, Rigoberto |
dc.contributor.author.none.fl_str_mv |
Caicedo Montoya, Carlos Manzo Ruiz, Monserrat Ríos Estepa, Rigoberto |
dc.subject.decs.none.fl_str_mv |
Streptomyces Genoma Genome |
topic |
Streptomyces Genoma Genome Compuestos bioactivos Bioactive compounds Pan-genome Genome mining Biosynthetic gene cluster Pangenoma http://aims.fao.org/aos/agrovoc/c_ec4deb8c |
dc.subject.agrovoc.none.fl_str_mv |
Compuestos bioactivos Bioactive compounds |
dc.subject.proposal.spa.fl_str_mv |
Pan-genome Genome mining Biosynthetic gene cluster Pangenoma |
dc.subject.agrovocuri.none.fl_str_mv |
http://aims.fao.org/aos/agrovoc/c_ec4deb8c |
description |
ABSTRACT: Species of the genus Streptomyces are known for their ability to produce multiple secondary metabolites; their genomes have been extensively explored to discover new bioactive compounds. The richness of genomic data currently available allows filtering for high quality genomes, which in turn permits reliable comparative genomics studies and an improved prediction of biosynthetic gene clusters (BGCs) through genome mining approaches. In this work, we used 121 genome sequences of the genus Streptomyces in a comparative genomics study with the aim of estimating the genomic diversity by protein domains content, sequence similarity of proteins and conservation of Intergenic Regions (IGRs). We also searched for BGCs but prioritizing those with potential antibiotic activity. Our analysis revealed that the pan-genome of the genus Streptomyces is clearly open, with a high quantity of unique gene families across the different species and that the IGRs are rarely conserved. We also described the phylogenetic relationships of the analyzed genomes using multiple markers, obtaining a trustworthy tree whose relationships were further validated by Average Nucleotide Identity (ANI) calculations. Finally, 33 biosynthetic gene clusters were detected to have potential antibiotic activity and a predicted mode of action, which might serve up as a guide to formulation of related experimental studies. |
publishDate |
2021 |
dc.date.accessioned.none.fl_str_mv |
2021-11-06T14:22:04Z |
dc.date.available.none.fl_str_mv |
2021-11-06T14:22:04Z |
dc.date.issued.none.fl_str_mv |
2021 |
dc.type.spa.fl_str_mv |
info:eu-repo/semantics/article |
dc.type.coarversion.fl_str_mv |
http://purl.org/coar/version/c_970fb48d4fbd8a85 |
dc.type.hasversion.spa.fl_str_mv |
info:eu-repo/semantics/publishedVersion |
dc.type.coar.spa.fl_str_mv |
http://purl.org/coar/resource_type/c_2df8fbb1 |
dc.type.redcol.spa.fl_str_mv |
https://purl.org/redcol/resource_type/ART |
dc.type.local.spa.fl_str_mv |
Artículo de investigación |
format |
http://purl.org/coar/resource_type/c_2df8fbb1 |
status_str |
publishedVersion |
dc.identifier.citation.spa.fl_str_mv |
Caicedo-Montoya C, Manzo-Ruiz M and Ríos-Estepa R (2021) Pan-Genome of the Genus Streptomyces and Prioritization of Biosynthetic Gene Clusters With Potential to Produce Antibiotic Compounds. Front. Microbiol. 12:677558. doi: 10.3389/fmicb.2021.677558 |
dc.identifier.issn.none.fl_str_mv |
1664-302X |
dc.identifier.uri.none.fl_str_mv |
http://hdl.handle.net/10495/23813 |
dc.identifier.doi.none.fl_str_mv |
10.3389/fmicb.2021.677558 |
identifier_str_mv |
Caicedo-Montoya C, Manzo-Ruiz M and Ríos-Estepa R (2021) Pan-Genome of the Genus Streptomyces and Prioritization of Biosynthetic Gene Clusters With Potential to Produce Antibiotic Compounds. Front. Microbiol. 12:677558. doi: 10.3389/fmicb.2021.677558 1664-302X 10.3389/fmicb.2021.677558 |
url |
http://hdl.handle.net/10495/23813 |
dc.language.iso.spa.fl_str_mv |
eng |
language |
eng |
dc.relation.ispartofjournalabbrev.spa.fl_str_mv |
Front. Microbiol. |
dc.rights.spa.fl_str_mv |
info:eu-repo/semantics/openAccess |
dc.rights.uri.*.fl_str_mv |
https://creativecommons.org/licenses/by/2.5/co/ |
dc.rights.accessrights.spa.fl_str_mv |
http://purl.org/coar/access_right/c_abf2 |
dc.rights.creativecommons.spa.fl_str_mv |
https://creativecommons.org/licenses/by-nc-nd/4.0/ |
eu_rights_str_mv |
openAccess |
rights_invalid_str_mv |
https://creativecommons.org/licenses/by/2.5/co/ http://purl.org/coar/access_right/c_abf2 https://creativecommons.org/licenses/by-nc-nd/4.0/ |
dc.format.extent.spa.fl_str_mv |
17 |
dc.format.mimetype.spa.fl_str_mv |
application/pdf |
dc.publisher.spa.fl_str_mv |
Frontiers Research Foundation |
dc.publisher.group.spa.fl_str_mv |
Bioprocesos |
dc.publisher.place.spa.fl_str_mv |
Lausana, Suiza |
institution |
Universidad de Antioquia |
bitstream.url.fl_str_mv |
http://bibliotecadigital.udea.edu.co/bitstream/10495/23813/1/CaicedoCarlos_RiosRigoberto_2021_PangenomeStreptomyces.pdf http://bibliotecadigital.udea.edu.co/bitstream/10495/23813/2/license_rdf http://bibliotecadigital.udea.edu.co/bitstream/10495/23813/3/license.txt |
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MD5 MD5 MD5 |
repository.name.fl_str_mv |
Repositorio Institucional Universidad de Antioquia |
repository.mail.fl_str_mv |
andres.perez@udea.edu.co |
_version_ |
1812173121986232320 |
spelling |
Caicedo Montoya, CarlosManzo Ruiz, MonserratRíos Estepa, Rigoberto2021-11-06T14:22:04Z2021-11-06T14:22:04Z2021Caicedo-Montoya C, Manzo-Ruiz M and Ríos-Estepa R (2021) Pan-Genome of the Genus Streptomyces and Prioritization of Biosynthetic Gene Clusters With Potential to Produce Antibiotic Compounds. Front. Microbiol. 12:677558. doi: 10.3389/fmicb.2021.6775581664-302Xhttp://hdl.handle.net/10495/2381310.3389/fmicb.2021.677558ABSTRACT: Species of the genus Streptomyces are known for their ability to produce multiple secondary metabolites; their genomes have been extensively explored to discover new bioactive compounds. The richness of genomic data currently available allows filtering for high quality genomes, which in turn permits reliable comparative genomics studies and an improved prediction of biosynthetic gene clusters (BGCs) through genome mining approaches. In this work, we used 121 genome sequences of the genus Streptomyces in a comparative genomics study with the aim of estimating the genomic diversity by protein domains content, sequence similarity of proteins and conservation of Intergenic Regions (IGRs). We also searched for BGCs but prioritizing those with potential antibiotic activity. Our analysis revealed that the pan-genome of the genus Streptomyces is clearly open, with a high quantity of unique gene families across the different species and that the IGRs are rarely conserved. We also described the phylogenetic relationships of the analyzed genomes using multiple markers, obtaining a trustworthy tree whose relationships were further validated by Average Nucleotide Identity (ANI) calculations. Finally, 33 biosynthetic gene clusters were detected to have potential antibiotic activity and a predicted mode of action, which might serve up as a guide to formulation of related experimental studies.COL002371517application/pdfengFrontiers Research FoundationBioprocesosLausana, Suizainfo:eu-repo/semantics/publishedVersioninfo:eu-repo/semantics/articlehttp://purl.org/coar/resource_type/c_2df8fbb1https://purl.org/redcol/resource_type/ARTArtículo de investigaciónhttp://purl.org/coar/version/c_970fb48d4fbd8a85info:eu-repo/semantics/openAccesshttps://creativecommons.org/licenses/by/2.5/co/http://purl.org/coar/access_right/c_abf2https://creativecommons.org/licenses/by-nc-nd/4.0/Pan-Genome of the Genus Streptomyces and Prioritization of Biosynthetic Gene Clusters With Potential to Produce Antibiotic CompoundsStreptomycesGenomaGenomeCompuestos bioactivosBioactive compoundsPan-genomeGenome miningBiosynthetic gene clusterPangenomahttp://aims.fao.org/aos/agrovoc/c_ec4deb8cFront. Microbiol.Frontiers in MicrobiologyORIGINALCaicedoCarlos_RiosRigoberto_2021_PangenomeStreptomyces.pdfCaicedoCarlos_RiosRigoberto_2021_PangenomeStreptomyces.pdfArtículo de investigaciónapplication/pdf9036096http://bibliotecadigital.udea.edu.co/bitstream/10495/23813/1/CaicedoCarlos_RiosRigoberto_2021_PangenomeStreptomyces.pdf4a73a3e34ebfa6eec4b1ecc5852c2047MD51CC-LICENSElicense_rdflicense_rdfapplication/rdf+xml; charset=utf-8823http://bibliotecadigital.udea.edu.co/bitstream/10495/23813/2/license_rdfb88b088d9957e670ce3b3fbe2eedbc13MD52LICENSElicense.txtlicense.txttext/plain; charset=utf-81748http://bibliotecadigital.udea.edu.co/bitstream/10495/23813/3/license.txt8a4605be74aa9ea9d79846c1fba20a33MD5310495/23813oai:bibliotecadigital.udea.edu.co:10495/238132021-11-06 10:18:08.994Repositorio Institucional Universidad de Antioquiaandres.perez@udea.edu.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 |