Characterization and comparative analysis of the genome of Puccinia sorghi Schwein, the causal agent of maize common rust

Autores
Rochi, Lucía; Dieguez, Maria Jose; Burguener, Germán; Darino, Martín Alejandro; Pergolesi, María Fernanda; Ingala, Lorena Romina; Cuyeu, Alba Romina; Turjanski, Adrián; Kreff, Enrique D.; Sacco, Francisco
Año de publicación
2018
Idioma
inglés
Tipo de recurso
artículo
Estado
versión publicada
Descripción
Rust fungi are one of the most devastating pathogens of crop plants. The biotrophic fungus Puccinia sorghi Schwein (Ps) is responsible for maize common rust, an endemic disease of maize (Zea mays L.) in Argentina that causes significant yield losses in corn production. In spite of this, the Ps genomic sequence was not available. We used Illumina sequencing to rapidly produce the 99.6 Mb draft genome sequence of Ps race RO10H11247, derived from a single-uredinial isolate from infected maize leaves collected in the Argentine Corn Belt Region during 2010. High quality reads were obtained from 200 bp paired-end and 5000 bp mate-paired libraries and assembled in 15,722 scaffolds. A pipeline which combined an ab initio program with homology-based models and homology to in planta enriched ESTs from four cereal pathogenic fungus (the three sequenced wheat rusts and Ustilago maydis) was used to identify 21,087 putative coding sequences, of which 1599 might be part of the Ps RO10H11247 secretome. Among the 458 highly conserved protein families from the euKaryotic Orthologous Groups (KOG) that occur in a wide range of eukaryotic organisms, 97.5% have at least one member with high homology in the Ps assembly (TBlastN, E-value ⩽ e−10) covering more than 50% of the length of the KOG protein. Comparative studies with the three sequenced wheat rust fungus, and microsynteny analysis involving Puccinia striiformis f. sp. tritici (Pst, wheat stripe rust fungus), support the quality achieved. The results presented here show the effectiveness of the Illumina strategy for sequencing dikaryotic genomes of non-model organisms and provides reliable DNA sequence information for genomic studies, including pathogenic mechanisms of this maize fungus and molecular marker design.
Instituto de Genética
Fil: Rochi, Lucía. Instituto Nacional de Tecnología Agropecuaria (INTA). Instituto de Genética; Argentina
Fil: Dieguez, María José. Instituto Nacional de Tecnología Agropecuaria (INTA). Instituto de Genética; Argentina
Fil: Burguener, Germán. Universidad de Buenos Aires. Facultad de Ciencias Exactas y Naturales; Argentina
Fil: Darino, Martín Alejandro. Instituto Nacional de Tecnología Agropecuaria (INTA). Instituto de Genética; Argentina
Fil: Pergolesi, Marí­a Fernanda. Instituto Nacional de Tecnología Agropecuaria (INTA). Instituto de Genética; Argentina
Fil: Ingala, Lorena Romina. Instituto Nacional de Tecnología Agropecuaria (INTA). Instituto de Genética; Argentina
Fil: Cuyeu, Alba Romina. Instituto Nacional de Tecnología Agropecuaria (INTA). Instituto de Genética; Argentina
Fil: Turjanski, Adrián. Universidad de Buenos Aires. Facultad de Ciencias Exactas y Naturales; Argentina
Fil: Kreff, Enrique D. Pioneer Hi-Bred International; Argentina
Fil: Sacco, Francisco. Instituto Nacional de Tecnología Agropecuaria (INTA). Instituto de Genética; Argentina
Fuente
Fungal Genetics and Biology 112 : 31-39 (Marzo 2018)
Materia
Genetic maps
Maize
Pathogens
Mapas Genéticos
Maíz
Zea mays
Puccinia sorghi
Organismos patógenos
Genome analysis
Análisis genómico
Nivel de accesibilidad
acceso restringido
Condiciones de uso
Repositorio
INTA Digital (INTA)
Institución
Instituto Nacional de Tecnología Agropecuaria
OAI Identificador
oai:localhost:20.500.12123/3698
Acceder
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oai_identifier_str oai:localhost:20.500.12123/3698
network_acronym_str INTADig
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network_name_str INTA Digital (INTA)
spelling Characterization and comparative analysis of the genome of Puccinia sorghi Schwein, the causal agent of maize common rustRochi, LucíaDieguez, Maria JoseBurguener, GermánDarino, Martín AlejandroPergolesi, María FernandaIngala, Lorena RominaCuyeu, Alba RominaTurjanski, AdriánKreff, Enrique D.Sacco, FranciscoGenetic mapsMaizePathogensMapas GenéticosMaízZea maysPuccinia sorghiOrganismos patógenosGenome analysisAnálisis genómicoRust fungi are one of the most devastating pathogens of crop plants. The biotrophic fungus Puccinia sorghi Schwein (Ps) is responsible for maize common rust, an endemic disease of maize (Zea mays L.) in Argentina that causes significant yield losses in corn production. In spite of this, the Ps genomic sequence was not available. We used Illumina sequencing to rapidly produce the 99.6 Mb draft genome sequence of Ps race RO10H11247, derived from a single-uredinial isolate from infected maize leaves collected in the Argentine Corn Belt Region during 2010. High quality reads were obtained from 200 bp paired-end and 5000 bp mate-paired libraries and assembled in 15,722 scaffolds. A pipeline which combined an ab initio program with homology-based models and homology to in planta enriched ESTs from four cereal pathogenic fungus (the three sequenced wheat rusts and Ustilago maydis) was used to identify 21,087 putative coding sequences, of which 1599 might be part of the Ps RO10H11247 secretome. Among the 458 highly conserved protein families from the euKaryotic Orthologous Groups (KOG) that occur in a wide range of eukaryotic organisms, 97.5% have at least one member with high homology in the Ps assembly (TBlastN, E-value ⩽ e−10) covering more than 50% of the length of the KOG protein. Comparative studies with the three sequenced wheat rust fungus, and microsynteny analysis involving Puccinia striiformis f. sp. tritici (Pst, wheat stripe rust fungus), support the quality achieved. The results presented here show the effectiveness of the Illumina strategy for sequencing dikaryotic genomes of non-model organisms and provides reliable DNA sequence information for genomic studies, including pathogenic mechanisms of this maize fungus and molecular marker design.Instituto de GenéticaFil: Rochi, Lucía. Instituto Nacional de Tecnología Agropecuaria (INTA). Instituto de Genética; ArgentinaFil: Dieguez, María José. Instituto Nacional de Tecnología Agropecuaria (INTA). Instituto de Genética; ArgentinaFil: Burguener, Germán. Universidad de Buenos Aires. Facultad de Ciencias Exactas y Naturales; ArgentinaFil: Darino, Martín Alejandro. Instituto Nacional de Tecnología Agropecuaria (INTA). Instituto de Genética; ArgentinaFil: Pergolesi, Marí­a Fernanda. Instituto Nacional de Tecnología Agropecuaria (INTA). Instituto de Genética; ArgentinaFil: Ingala, Lorena Romina. Instituto Nacional de Tecnología Agropecuaria (INTA). Instituto de Genética; ArgentinaFil: Cuyeu, Alba Romina. Instituto Nacional de Tecnología Agropecuaria (INTA). Instituto de Genética; ArgentinaFil: Turjanski, Adrián. Universidad de Buenos Aires. Facultad de Ciencias Exactas y Naturales; ArgentinaFil: Kreff, Enrique D. Pioneer Hi-Bred International; ArgentinaFil: Sacco, Francisco. Instituto Nacional de Tecnología Agropecuaria (INTA). Instituto de Genética; ArgentinaElsevier2018-10-24T17:23:29Z2018-10-24T17:23:29Z2018-03info:eu-repo/semantics/articleinfo:eu-repo/semantics/publishedVersionhttp://purl.org/coar/resource_type/c_6501info:ar-repo/semantics/articuloapplication/pdfhttps://www.sciencedirect.com/science/article/pii/S1087184516301098?via%3Dihubhttp://hdl.handle.net/20.500.12123/36981087-1845http://dx.doi.org/10.1016/j.fgb.2016.10.001Fungal Genetics and Biology 112 : 31-39 (Marzo 2018)reponame:INTA Digital (INTA)instname:Instituto Nacional de Tecnología Agropecuariaenginfo:eu-repograntAgreement/INTA/PNBIO/1131042/AR./Genómica aplicada al mejoramiento molecular.info:eu-repo/semantics/restrictedAccess2025-09-29T13:44:28Zoai:localhost:20.500.12123/3698instacron:INTAInstitucionalhttp://repositorio.inta.gob.ar/Organismo científico-tecnológicoNo correspondehttp://repositorio.inta.gob.ar/oai/requesttripaldi.nicolas@inta.gob.arArgentinaNo correspondeNo correspondeNo correspondeopendoar:l2025-09-29 13:44:28.614INTA Digital (INTA) - Instituto Nacional de Tecnología Agropecuariafalse
dc.title.none.fl_str_mv Characterization and comparative analysis of the genome of Puccinia sorghi Schwein, the causal agent of maize common rust
title Characterization and comparative analysis of the genome of Puccinia sorghi Schwein, the causal agent of maize common rust
spellingShingle Characterization and comparative analysis of the genome of Puccinia sorghi Schwein, the causal agent of maize common rust
Rochi, Lucía
Genetic maps
Maize
Pathogens
Mapas Genéticos
Maíz
Zea mays
Puccinia sorghi
Organismos patógenos
Genome analysis
Análisis genómico
title_short Characterization and comparative analysis of the genome of Puccinia sorghi Schwein, the causal agent of maize common rust
title_full Characterization and comparative analysis of the genome of Puccinia sorghi Schwein, the causal agent of maize common rust
title_fullStr Characterization and comparative analysis of the genome of Puccinia sorghi Schwein, the causal agent of maize common rust
title_full_unstemmed Characterization and comparative analysis of the genome of Puccinia sorghi Schwein, the causal agent of maize common rust
title_sort Characterization and comparative analysis of the genome of Puccinia sorghi Schwein, the causal agent of maize common rust
dc.creator.none.fl_str_mv Rochi, Lucía
Dieguez, Maria Jose
Burguener, Germán
Darino, Martín Alejandro
Pergolesi, María Fernanda
Ingala, Lorena Romina
Cuyeu, Alba Romina
Turjanski, Adrián
Kreff, Enrique D.
Sacco, Francisco
author Rochi, Lucía
author_facet Rochi, Lucía
Dieguez, Maria Jose
Burguener, Germán
Darino, Martín Alejandro
Pergolesi, María Fernanda
Ingala, Lorena Romina
Cuyeu, Alba Romina
Turjanski, Adrián
Kreff, Enrique D.
Sacco, Francisco
author_role author
author2 Dieguez, Maria Jose
Burguener, Germán
Darino, Martín Alejandro
Pergolesi, María Fernanda
Ingala, Lorena Romina
Cuyeu, Alba Romina
Turjanski, Adrián
Kreff, Enrique D.
Sacco, Francisco
author2_role author
author
author
author
author
author
author
author
author
dc.subject.none.fl_str_mv Genetic maps
Maize
Pathogens
Mapas Genéticos
Maíz
Zea mays
Puccinia sorghi
Organismos patógenos
Genome analysis
Análisis genómico
topic Genetic maps
Maize
Pathogens
Mapas Genéticos
Maíz
Zea mays
Puccinia sorghi
Organismos patógenos
Genome analysis
Análisis genómico
dc.description.none.fl_txt_mv Rust fungi are one of the most devastating pathogens of crop plants. The biotrophic fungus Puccinia sorghi Schwein (Ps) is responsible for maize common rust, an endemic disease of maize (Zea mays L.) in Argentina that causes significant yield losses in corn production. In spite of this, the Ps genomic sequence was not available. We used Illumina sequencing to rapidly produce the 99.6 Mb draft genome sequence of Ps race RO10H11247, derived from a single-uredinial isolate from infected maize leaves collected in the Argentine Corn Belt Region during 2010. High quality reads were obtained from 200 bp paired-end and 5000 bp mate-paired libraries and assembled in 15,722 scaffolds. A pipeline which combined an ab initio program with homology-based models and homology to in planta enriched ESTs from four cereal pathogenic fungus (the three sequenced wheat rusts and Ustilago maydis) was used to identify 21,087 putative coding sequences, of which 1599 might be part of the Ps RO10H11247 secretome. Among the 458 highly conserved protein families from the euKaryotic Orthologous Groups (KOG) that occur in a wide range of eukaryotic organisms, 97.5% have at least one member with high homology in the Ps assembly (TBlastN, E-value ⩽ e−10) covering more than 50% of the length of the KOG protein. Comparative studies with the three sequenced wheat rust fungus, and microsynteny analysis involving Puccinia striiformis f. sp. tritici (Pst, wheat stripe rust fungus), support the quality achieved. The results presented here show the effectiveness of the Illumina strategy for sequencing dikaryotic genomes of non-model organisms and provides reliable DNA sequence information for genomic studies, including pathogenic mechanisms of this maize fungus and molecular marker design.
Instituto de Genética
Fil: Rochi, Lucía. Instituto Nacional de Tecnología Agropecuaria (INTA). Instituto de Genética; Argentina
Fil: Dieguez, María José. Instituto Nacional de Tecnología Agropecuaria (INTA). Instituto de Genética; Argentina
Fil: Burguener, Germán. Universidad de Buenos Aires. Facultad de Ciencias Exactas y Naturales; Argentina
Fil: Darino, Martín Alejandro. Instituto Nacional de Tecnología Agropecuaria (INTA). Instituto de Genética; Argentina
Fil: Pergolesi, Marí­a Fernanda. Instituto Nacional de Tecnología Agropecuaria (INTA). Instituto de Genética; Argentina
Fil: Ingala, Lorena Romina. Instituto Nacional de Tecnología Agropecuaria (INTA). Instituto de Genética; Argentina
Fil: Cuyeu, Alba Romina. Instituto Nacional de Tecnología Agropecuaria (INTA). Instituto de Genética; Argentina
Fil: Turjanski, Adrián. Universidad de Buenos Aires. Facultad de Ciencias Exactas y Naturales; Argentina
Fil: Kreff, Enrique D. Pioneer Hi-Bred International; Argentina
Fil: Sacco, Francisco. Instituto Nacional de Tecnología Agropecuaria (INTA). Instituto de Genética; Argentina
description Rust fungi are one of the most devastating pathogens of crop plants. The biotrophic fungus Puccinia sorghi Schwein (Ps) is responsible for maize common rust, an endemic disease of maize (Zea mays L.) in Argentina that causes significant yield losses in corn production. In spite of this, the Ps genomic sequence was not available. We used Illumina sequencing to rapidly produce the 99.6 Mb draft genome sequence of Ps race RO10H11247, derived from a single-uredinial isolate from infected maize leaves collected in the Argentine Corn Belt Region during 2010. High quality reads were obtained from 200 bp paired-end and 5000 bp mate-paired libraries and assembled in 15,722 scaffolds. A pipeline which combined an ab initio program with homology-based models and homology to in planta enriched ESTs from four cereal pathogenic fungus (the three sequenced wheat rusts and Ustilago maydis) was used to identify 21,087 putative coding sequences, of which 1599 might be part of the Ps RO10H11247 secretome. Among the 458 highly conserved protein families from the euKaryotic Orthologous Groups (KOG) that occur in a wide range of eukaryotic organisms, 97.5% have at least one member with high homology in the Ps assembly (TBlastN, E-value ⩽ e−10) covering more than 50% of the length of the KOG protein. Comparative studies with the three sequenced wheat rust fungus, and microsynteny analysis involving Puccinia striiformis f. sp. tritici (Pst, wheat stripe rust fungus), support the quality achieved. The results presented here show the effectiveness of the Illumina strategy for sequencing dikaryotic genomes of non-model organisms and provides reliable DNA sequence information for genomic studies, including pathogenic mechanisms of this maize fungus and molecular marker design.
publishDate 2018
dc.date.none.fl_str_mv 2018-10-24T17:23:29Z
2018-10-24T17:23:29Z
2018-03
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 https://www.sciencedirect.com/science/article/pii/S1087184516301098?via%3Dihub
http://hdl.handle.net/20.500.12123/3698
1087-1845
http://dx.doi.org/10.1016/j.fgb.2016.10.001
url https://www.sciencedirect.com/science/article/pii/S1087184516301098?via%3Dihub
http://hdl.handle.net/20.500.12123/3698
http://dx.doi.org/10.1016/j.fgb.2016.10.001
identifier_str_mv 1087-1845
dc.language.none.fl_str_mv eng
language eng
dc.relation.none.fl_str_mv info:eu-repograntAgreement/INTA/PNBIO/1131042/AR./Genómica aplicada al mejoramiento molecular.
dc.rights.none.fl_str_mv info:eu-repo/semantics/restrictedAccess
eu_rights_str_mv restrictedAccess
dc.format.none.fl_str_mv application/pdf
dc.publisher.none.fl_str_mv Elsevier
publisher.none.fl_str_mv Elsevier
dc.source.none.fl_str_mv Fungal Genetics and Biology 112 : 31-39 (Marzo 2018)
reponame:INTA Digital (INTA)
instname:Instituto Nacional de Tecnología Agropecuaria
reponame_str INTA Digital (INTA)
collection INTA Digital (INTA)
instname_str Instituto Nacional de Tecnología Agropecuaria
repository.name.fl_str_mv INTA Digital (INTA) - Instituto Nacional de Tecnología Agropecuaria
repository.mail.fl_str_mv tripaldi.nicolas@inta.gob.ar
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score 12.559606

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