Gene regulatory network inference and gene module regulating virulence in Fusarium oxysporum

In this work, we inferred the gene regulatory network (GRN) of the fungus Fusarium oxysporum by using the regulatory networks of Aspergillus nidulans FGSC A4, Neurospora crassa OR74A, Saccharomyces cerevisiae S288c, and Fusarium graminearum PH-1 as templates for sequence comparisons. Topological pro...

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Detalhes bibliográficos
Autores: REGNIER CANO, Alexandre Rafael Lenz, EDGARDO GALAN VASQUEZ, Jorge Humberto Ramírez Prado, ERNESTO PEREZ RUEDA
Formato: artículo
Estado:Versión publicada
Fecha de publicación:2022
País:México
Recursos:Centro de Investigación Científica de Yucatán
Repositorio:Repositorio Institucional CICY
Idioma:inglés
OAI Identifier:oai:cicy.repositorioinstitucional.mx:1003/2803
Acesso em linha:http://cicy.repositorioinstitucional.mx/jspui/handle/1003/2803
Access Level:acceso abierto
Palavra-chave:info:eu-repo/classification/Autores/FUSARIUM OXYSPORUM
info:eu-repo/classification/Autores/VIRULENCE
info:eu-repo/classification/Autores/GENE REGULATION
info:eu-repo/classification/Autores/REGULATORY NETWORKS
info:eu-repo/classification/Autores/TRANSCRIPTION FACTORS
info:eu-repo/classification/Autores/COMPARATIVE GENOMICS
info:eu-repo/classification/cti/2
info:eu-repo/classification/cti/24
info:eu-repo/classification/cti/2415
info:eu-repo/classification/cti/241502
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spelling Gene regulatory network inference and gene module regulating virulence in Fusarium oxysporumREGNIER CANOAlexandre Rafael LenzEDGARDO GALAN VASQUEZJorge Humberto Ramírez PradoERNESTO PEREZ RUEDAinfo:eu-repo/classification/Autores/FUSARIUM OXYSPORUMinfo:eu-repo/classification/Autores/VIRULENCEinfo:eu-repo/classification/Autores/GENE REGULATIONinfo:eu-repo/classification/Autores/REGULATORY NETWORKSinfo:eu-repo/classification/Autores/TRANSCRIPTION FACTORSinfo:eu-repo/classification/Autores/COMPARATIVE GENOMICSinfo:eu-repo/classification/cti/2info:eu-repo/classification/cti/24info:eu-repo/classification/cti/2415info:eu-repo/classification/cti/241502info:eu-repo/classification/cti/241502In this work, we inferred the gene regulatory network (GRN) of the fungus Fusarium oxysporum by using the regulatory networks of Aspergillus nidulans FGSC A4, Neurospora crassa OR74A, Saccharomyces cerevisiae S288c, and Fusarium graminearum PH-1 as templates for sequence comparisons. Topological properties to infer the role of transcription factors (TFs) and to identify functional modules were calculated in the GRN. From these analyzes, five TFs were identified as hubs, including FOXG_04688 and FOXG_05432, which regulate 2,404 and 1,864 target genes, respectively. In addition, 16 communities were identified in the GRN, where the largest contains 1,923 genes and the smallest contains 227 genes. Finally, the genes associated with virulence were extracted from the GRN and exhaustively analyzed, and we identified a giant module with ten TFs and 273 target genes, where the most highly connected node corresponds to the transcription factor FOXG_05265, homologous to the putative bZip transcription factor CPTF1 of Claviceps purpurea, which is involved in ergotism disease that affects cereal crops and grasses. The results described in this work can be used for the study of gene regulation in this organism and open the possibility to explore putative genes associated with virulence against their host. Copyright © 2022 Cano, Lenz, Galan-Vasquez, Ramirez-Prado and Perez-Rueda.2022info:eu-repo/semantics/articleinfo:eu-repo/semantics/publishedVersionapplication/pdfhttp://cicy.repositorioinstitucional.mx/jspui/handle/1003/2803Frontiers in Microbiology, 13, 2022.reponame:Repositorio Institucional CICYinstname:Centro de Investigación Científica de Yucatáninstacron:CICYenginfo:eu-repo/semantics/datasetDOI/doi: 10.3389/fmicb.2022.861528citation:Cano, R., Lenz, A. R., Galan-Vasquez, E., Ramirez-Prado, J. H., & Perez-Rueda, E. (2022). Gene regulatory network inference and gene module regulating virulence in Fusarium oxysporum. Frontiers in Microbiology, 13.info:eu-repo/semantics/openAccesshttp://creativecommons.org/licenses/by-nc-nd/4.0oai:cicy.repositorioinstitucional.mx:1003/28032024-08-28T03:19:25Z
dc.title.none.fl_str_mv Gene regulatory network inference and gene module regulating virulence in Fusarium oxysporum
title Gene regulatory network inference and gene module regulating virulence in Fusarium oxysporum
spellingShingle Gene regulatory network inference and gene module regulating virulence in Fusarium oxysporum
REGNIER CANO
info:eu-repo/classification/Autores/FUSARIUM OXYSPORUM
info:eu-repo/classification/Autores/VIRULENCE
info:eu-repo/classification/Autores/GENE REGULATION
info:eu-repo/classification/Autores/REGULATORY NETWORKS
info:eu-repo/classification/Autores/TRANSCRIPTION FACTORS
info:eu-repo/classification/Autores/COMPARATIVE GENOMICS
info:eu-repo/classification/cti/2
info:eu-repo/classification/cti/24
info:eu-repo/classification/cti/2415
info:eu-repo/classification/cti/241502
info:eu-repo/classification/cti/241502
title_short Gene regulatory network inference and gene module regulating virulence in Fusarium oxysporum
title_full Gene regulatory network inference and gene module regulating virulence in Fusarium oxysporum
title_fullStr Gene regulatory network inference and gene module regulating virulence in Fusarium oxysporum
title_full_unstemmed Gene regulatory network inference and gene module regulating virulence in Fusarium oxysporum
title_sort Gene regulatory network inference and gene module regulating virulence in Fusarium oxysporum
dc.creator.none.fl_str_mv REGNIER CANO
Alexandre Rafael Lenz
EDGARDO GALAN VASQUEZ
Jorge Humberto Ramírez Prado
ERNESTO PEREZ RUEDA
author REGNIER CANO
author_facet REGNIER CANO
Alexandre Rafael Lenz
EDGARDO GALAN VASQUEZ
Jorge Humberto Ramírez Prado
ERNESTO PEREZ RUEDA
author_role author
author2 Alexandre Rafael Lenz
EDGARDO GALAN VASQUEZ
Jorge Humberto Ramírez Prado
ERNESTO PEREZ RUEDA
author2_role author
author
author
author
dc.subject.none.fl_str_mv info:eu-repo/classification/Autores/FUSARIUM OXYSPORUM
info:eu-repo/classification/Autores/VIRULENCE
info:eu-repo/classification/Autores/GENE REGULATION
info:eu-repo/classification/Autores/REGULATORY NETWORKS
info:eu-repo/classification/Autores/TRANSCRIPTION FACTORS
info:eu-repo/classification/Autores/COMPARATIVE GENOMICS
info:eu-repo/classification/cti/2
info:eu-repo/classification/cti/24
info:eu-repo/classification/cti/2415
info:eu-repo/classification/cti/241502
info:eu-repo/classification/cti/241502
topic info:eu-repo/classification/Autores/FUSARIUM OXYSPORUM
info:eu-repo/classification/Autores/VIRULENCE
info:eu-repo/classification/Autores/GENE REGULATION
info:eu-repo/classification/Autores/REGULATORY NETWORKS
info:eu-repo/classification/Autores/TRANSCRIPTION FACTORS
info:eu-repo/classification/Autores/COMPARATIVE GENOMICS
info:eu-repo/classification/cti/2
info:eu-repo/classification/cti/24
info:eu-repo/classification/cti/2415
info:eu-repo/classification/cti/241502
info:eu-repo/classification/cti/241502
description In this work, we inferred the gene regulatory network (GRN) of the fungus Fusarium oxysporum by using the regulatory networks of Aspergillus nidulans FGSC A4, Neurospora crassa OR74A, Saccharomyces cerevisiae S288c, and Fusarium graminearum PH-1 as templates for sequence comparisons. Topological properties to infer the role of transcription factors (TFs) and to identify functional modules were calculated in the GRN. From these analyzes, five TFs were identified as hubs, including FOXG_04688 and FOXG_05432, which regulate 2,404 and 1,864 target genes, respectively. In addition, 16 communities were identified in the GRN, where the largest contains 1,923 genes and the smallest contains 227 genes. Finally, the genes associated with virulence were extracted from the GRN and exhaustively analyzed, and we identified a giant module with ten TFs and 273 target genes, where the most highly connected node corresponds to the transcription factor FOXG_05265, homologous to the putative bZip transcription factor CPTF1 of Claviceps purpurea, which is involved in ergotism disease that affects cereal crops and grasses. The results described in this work can be used for the study of gene regulation in this organism and open the possibility to explore putative genes associated with virulence against their host. Copyright © 2022 Cano, Lenz, Galan-Vasquez, Ramirez-Prado and Perez-Rueda.
publishDate 2022
dc.date.none.fl_str_mv 2022
dc.type.none.fl_str_mv info:eu-repo/semantics/article
info:eu-repo/semantics/publishedVersion
format article
status_str publishedVersion
dc.identifier.none.fl_str_mv http://cicy.repositorioinstitucional.mx/jspui/handle/1003/2803
url http://cicy.repositorioinstitucional.mx/jspui/handle/1003/2803
dc.language.none.fl_str_mv eng
language eng
dc.relation.none.fl_str_mv info:eu-repo/semantics/datasetDOI/doi: 10.3389/fmicb.2022.861528
citation:Cano, R., Lenz, A. R., Galan-Vasquez, E., Ramirez-Prado, J. H., & Perez-Rueda, E. (2022). Gene regulatory network inference and gene module regulating virulence in Fusarium oxysporum. Frontiers in Microbiology, 13.
dc.rights.none.fl_str_mv info:eu-repo/semantics/openAccess
http://creativecommons.org/licenses/by-nc-nd/4.0
eu_rights_str_mv openAccess
rights_invalid_str_mv http://creativecommons.org/licenses/by-nc-nd/4.0
dc.format.none.fl_str_mv application/pdf
dc.source.none.fl_str_mv Frontiers in Microbiology, 13, 2022.
reponame:Repositorio Institucional CICY
instname:Centro de Investigación Científica de Yucatán
instacron:CICY
instname_str Centro de Investigación Científica de Yucatán
instacron_str CICY
institution CICY
reponame_str Repositorio Institucional CICY
collection Repositorio Institucional CICY
repository.name.fl_str_mv
repository.mail.fl_str_mv
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score 15.812429

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