Developing a Pan-Genome of the diplosporous grass Eragrostis curvula

Autores
Bongiorno, G.; Carballo, José; Gallo, Cristian Andrés; Albertini, Emiliano; Zappacosta, Diego Carlos; Echenique, Carmen Viviana
Año de publicación
2023
Idioma
inglés
Tipo de recurso
documento de conferencia
Estado
versión publicada
Descripción
As large-scale genomic studies have progressed, it has been revealed that a single reference genome patterncannot represent the genetic diversity present at the species level. The pangenome can complement themissing genetic information based on the analysis of a single reference genome, exhibit hidden geneticvariations, and demonstrate the true genetic diversity at the species level. The progress of pangenomeresearch in different species has allowed the identification of large structural variants related to importantagronomic traits. Weeping lovegrass (Eragrostis curvula [Schrad.] Nees) is a forage grass that reproduces bysexuality and by facultative and obligate apomixis. It presents distinctive variants with different ploidy levels(2x – 8x) and a basic chromosome number of 10. The recent availability of the genome assembly of cv.Victoria has provided a valuable resource for identifying specific genomic regions linked to significant traits,for instance, forage quality. However, it is worth noting that the regions that control apomixis and othersrelated with ploidy are typically hosted by genotypes with higher ploidy levels. In this work, we focused on constructing a pan-genome of Eragrostis curvula to detect genomic variation,establish phylogenetic relationships, and analyze the effects of ploidy in genome evolution and reproductivemode. To do that, we used the genome assembly of cv. Victoria and genomic data, obtained by Illumina reads,of nine genetically diverse accessions of E. curvula. The construction of the pan-genome employed an iterativemapping and assembly approach involving the mapping of reads from different genotypes to the referencegenome assembly. The mapped reads were used for variant calling, while the unmapped reads wereassembled into new genomic fragments to annotate genes absent in the reference genome. These newlyassembled sequences were subsequently integrated into the reference genome, and the process was repeatediteratively for other genotypes. When all the accessions were processed, the final pan-genome comprised thereference genome and the newly assembled sequences. This approach proved to be highly efficient forconstructing a pan-genome exploiting the reference genome and the assembly of genetically distantgenotypes of E. curvula. Ultimately, the genomic resources generated were employed to gain a comprehensiveunderstanding of the genetic mechanisms underlying apomixis and related processes.
Fil: Bongiorno, G.. Università di Perugia; Italia
Fil: Carballo, José. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Bahía Blanca. Centro de Recursos Naturales Renovables de la Zona Semiárida. Universidad Nacional del Sur. Centro de Recursos Naturales Renovables de la Zona Semiárida; Argentina. Universidad Nacional del Sur. Departamento de Agronomía; Argentina
Fil: Gallo, Cristian Andrés. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Bahía Blanca. Centro de Recursos Naturales Renovables de la Zona Semiárida. Universidad Nacional del Sur. Centro de Recursos Naturales Renovables de la Zona Semiárida; Argentina
Fil: Albertini, Emiliano. Università di Perugia; Italia
Fil: Zappacosta, Diego Carlos. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Bahía Blanca. Centro de Recursos Naturales Renovables de la Zona Semiárida. Universidad Nacional del Sur. Centro de Recursos Naturales Renovables de la Zona Semiárida; Argentina. Universidad Nacional del Sur. Departamento de Agronomía; Argentina
Fil: Echenique, Carmen Viviana. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Bahía Blanca. Centro de Recursos Naturales Renovables de la Zona Semiárida. Universidad Nacional del Sur. Centro de Recursos Naturales Renovables de la Zona Semiárida; Argentina. Universidad Nacional del Sur. Departamento de Agronomía; Argentina
IV International Congress on Apomixis
Rosario
Argentina
Committee Organisation of IV International Congress on Apomixis
Materia
APOMIXIS
PANGENOME
NGS
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:11336/241146
Acceder
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network_name_str CONICET Digital (CONICET)
spelling Developing a Pan-Genome of the diplosporous grass Eragrostis curvulaBongiorno, G.Carballo, JoséGallo, Cristian AndrésAlbertini, EmilianoZappacosta, Diego CarlosEchenique, Carmen VivianaAPOMIXISPANGENOMENGShttps://purl.org/becyt/ford/4.4https://purl.org/becyt/ford/4As large-scale genomic studies have progressed, it has been revealed that a single reference genome patterncannot represent the genetic diversity present at the species level. The pangenome can complement themissing genetic information based on the analysis of a single reference genome, exhibit hidden geneticvariations, and demonstrate the true genetic diversity at the species level. The progress of pangenomeresearch in different species has allowed the identification of large structural variants related to importantagronomic traits. Weeping lovegrass (Eragrostis curvula [Schrad.] Nees) is a forage grass that reproduces bysexuality and by facultative and obligate apomixis. It presents distinctive variants with different ploidy levels(2x – 8x) and a basic chromosome number of 10. The recent availability of the genome assembly of cv.Victoria has provided a valuable resource for identifying specific genomic regions linked to significant traits,for instance, forage quality. However, it is worth noting that the regions that control apomixis and othersrelated with ploidy are typically hosted by genotypes with higher ploidy levels. In this work, we focused on constructing a pan-genome of Eragrostis curvula to detect genomic variation,establish phylogenetic relationships, and analyze the effects of ploidy in genome evolution and reproductivemode. To do that, we used the genome assembly of cv. Victoria and genomic data, obtained by Illumina reads,of nine genetically diverse accessions of E. curvula. The construction of the pan-genome employed an iterativemapping and assembly approach involving the mapping of reads from different genotypes to the referencegenome assembly. The mapped reads were used for variant calling, while the unmapped reads wereassembled into new genomic fragments to annotate genes absent in the reference genome. These newlyassembled sequences were subsequently integrated into the reference genome, and the process was repeatediteratively for other genotypes. When all the accessions were processed, the final pan-genome comprised thereference genome and the newly assembled sequences. This approach proved to be highly efficient forconstructing a pan-genome exploiting the reference genome and the assembly of genetically distantgenotypes of E. curvula. Ultimately, the genomic resources generated were employed to gain a comprehensiveunderstanding of the genetic mechanisms underlying apomixis and related processes.Fil: Bongiorno, G.. Università di Perugia; ItaliaFil: Carballo, José. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Bahía Blanca. Centro de Recursos Naturales Renovables de la Zona Semiárida. Universidad Nacional del Sur. Centro de Recursos Naturales Renovables de la Zona Semiárida; Argentina. Universidad Nacional del Sur. Departamento de Agronomía; ArgentinaFil: Gallo, Cristian Andrés. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Bahía Blanca. Centro de Recursos Naturales Renovables de la Zona Semiárida. Universidad Nacional del Sur. Centro de Recursos Naturales Renovables de la Zona Semiárida; ArgentinaFil: Albertini, Emiliano. Università di Perugia; ItaliaFil: Zappacosta, Diego Carlos. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Bahía Blanca. Centro de Recursos Naturales Renovables de la Zona Semiárida. Universidad Nacional del Sur. Centro de Recursos Naturales Renovables de la Zona Semiárida; Argentina. Universidad Nacional del Sur. Departamento de Agronomía; ArgentinaFil: Echenique, Carmen Viviana. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Bahía Blanca. Centro de Recursos Naturales Renovables de la Zona Semiárida. Universidad Nacional del Sur. Centro de Recursos Naturales Renovables de la Zona Semiárida; Argentina. Universidad Nacional del Sur. Departamento de Agronomía; ArgentinaIV International Congress on ApomixisRosarioArgentinaCommittee Organisation of IV International Congress on ApomixisCommittee Organisation of IV International Congress on Apomixis2023info:eu-repo/semantics/publishedVersioninfo:eu-repo/semantics/conferenceObjectCongresoBookhttp://purl.org/coar/resource_type/c_5794info:ar-repo/semantics/documentoDeConferenciaapplication/pdfapplication/pdfapplication/pdfhttp://hdl.handle.net/11336/241146Developing a Pan-Genome of the diplosporous grass Eragrostis curvula; IV International Congress on Apomixis; Rosario; Argentina; 2023; 31-31CONICET DigitalCONICETenginfo:eu-repo/semantics/altIdentifier/url/https://apomixis2023.com.ar/wp-content/uploads/APOMIXIS-2023-book-of-abstracts.pdfInternacionalinfo:eu-repo/semantics/openAccesshttps://creativecommons.org/licenses/by-nc-sa/2.5/ar/reponame:CONICET Digital (CONICET)instname:Consejo Nacional de Investigaciones Científicas y Técnicas2025-09-29T10:35:08Zoai:ri.conicet.gov.ar:11336/241146instacron: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:34982025-09-29 10:35:08.361CONICET Digital (CONICET) - Consejo Nacional de Investigaciones Científicas y Técnicasfalse
dc.title.none.fl_str_mv Developing a Pan-Genome of the diplosporous grass Eragrostis curvula
title Developing a Pan-Genome of the diplosporous grass Eragrostis curvula
spellingShingle Developing a Pan-Genome of the diplosporous grass Eragrostis curvula
Bongiorno, G.
APOMIXIS
PANGENOME
NGS
title_short Developing a Pan-Genome of the diplosporous grass Eragrostis curvula
title_full Developing a Pan-Genome of the diplosporous grass Eragrostis curvula
title_fullStr Developing a Pan-Genome of the diplosporous grass Eragrostis curvula
title_full_unstemmed Developing a Pan-Genome of the diplosporous grass Eragrostis curvula
title_sort Developing a Pan-Genome of the diplosporous grass Eragrostis curvula
dc.creator.none.fl_str_mv Bongiorno, G.
Carballo, José
Gallo, Cristian Andrés
Albertini, Emiliano
Zappacosta, Diego Carlos
Echenique, Carmen Viviana
author Bongiorno, G.
author_facet Bongiorno, G.
Carballo, José
Gallo, Cristian Andrés
Albertini, Emiliano
Zappacosta, Diego Carlos
Echenique, Carmen Viviana
author_role author
author2 Carballo, José
Gallo, Cristian Andrés
Albertini, Emiliano
Zappacosta, Diego Carlos
Echenique, Carmen Viviana
author2_role author
author
author
author
author
dc.subject.none.fl_str_mv APOMIXIS
PANGENOME
NGS
topic APOMIXIS
PANGENOME
NGS
purl_subject.fl_str_mv https://purl.org/becyt/ford/4.4
https://purl.org/becyt/ford/4
dc.description.none.fl_txt_mv As large-scale genomic studies have progressed, it has been revealed that a single reference genome patterncannot represent the genetic diversity present at the species level. The pangenome can complement themissing genetic information based on the analysis of a single reference genome, exhibit hidden geneticvariations, and demonstrate the true genetic diversity at the species level. The progress of pangenomeresearch in different species has allowed the identification of large structural variants related to importantagronomic traits. Weeping lovegrass (Eragrostis curvula [Schrad.] Nees) is a forage grass that reproduces bysexuality and by facultative and obligate apomixis. It presents distinctive variants with different ploidy levels(2x – 8x) and a basic chromosome number of 10. The recent availability of the genome assembly of cv.Victoria has provided a valuable resource for identifying specific genomic regions linked to significant traits,for instance, forage quality. However, it is worth noting that the regions that control apomixis and othersrelated with ploidy are typically hosted by genotypes with higher ploidy levels. In this work, we focused on constructing a pan-genome of Eragrostis curvula to detect genomic variation,establish phylogenetic relationships, and analyze the effects of ploidy in genome evolution and reproductivemode. To do that, we used the genome assembly of cv. Victoria and genomic data, obtained by Illumina reads,of nine genetically diverse accessions of E. curvula. The construction of the pan-genome employed an iterativemapping and assembly approach involving the mapping of reads from different genotypes to the referencegenome assembly. The mapped reads were used for variant calling, while the unmapped reads wereassembled into new genomic fragments to annotate genes absent in the reference genome. These newlyassembled sequences were subsequently integrated into the reference genome, and the process was repeatediteratively for other genotypes. When all the accessions were processed, the final pan-genome comprised thereference genome and the newly assembled sequences. This approach proved to be highly efficient forconstructing a pan-genome exploiting the reference genome and the assembly of genetically distantgenotypes of E. curvula. Ultimately, the genomic resources generated were employed to gain a comprehensiveunderstanding of the genetic mechanisms underlying apomixis and related processes.
Fil: Bongiorno, G.. Università di Perugia; Italia
Fil: Carballo, José. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Bahía Blanca. Centro de Recursos Naturales Renovables de la Zona Semiárida. Universidad Nacional del Sur. Centro de Recursos Naturales Renovables de la Zona Semiárida; Argentina. Universidad Nacional del Sur. Departamento de Agronomía; Argentina
Fil: Gallo, Cristian Andrés. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Bahía Blanca. Centro de Recursos Naturales Renovables de la Zona Semiárida. Universidad Nacional del Sur. Centro de Recursos Naturales Renovables de la Zona Semiárida; Argentina
Fil: Albertini, Emiliano. Università di Perugia; Italia
Fil: Zappacosta, Diego Carlos. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Bahía Blanca. Centro de Recursos Naturales Renovables de la Zona Semiárida. Universidad Nacional del Sur. Centro de Recursos Naturales Renovables de la Zona Semiárida; Argentina. Universidad Nacional del Sur. Departamento de Agronomía; Argentina
Fil: Echenique, Carmen Viviana. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Bahía Blanca. Centro de Recursos Naturales Renovables de la Zona Semiárida. Universidad Nacional del Sur. Centro de Recursos Naturales Renovables de la Zona Semiárida; Argentina. Universidad Nacional del Sur. Departamento de Agronomía; Argentina
IV International Congress on Apomixis
Rosario
Argentina
Committee Organisation of IV International Congress on Apomixis
description As large-scale genomic studies have progressed, it has been revealed that a single reference genome patterncannot represent the genetic diversity present at the species level. The pangenome can complement themissing genetic information based on the analysis of a single reference genome, exhibit hidden geneticvariations, and demonstrate the true genetic diversity at the species level. The progress of pangenomeresearch in different species has allowed the identification of large structural variants related to importantagronomic traits. Weeping lovegrass (Eragrostis curvula [Schrad.] Nees) is a forage grass that reproduces bysexuality and by facultative and obligate apomixis. It presents distinctive variants with different ploidy levels(2x – 8x) and a basic chromosome number of 10. The recent availability of the genome assembly of cv.Victoria has provided a valuable resource for identifying specific genomic regions linked to significant traits,for instance, forage quality. However, it is worth noting that the regions that control apomixis and othersrelated with ploidy are typically hosted by genotypes with higher ploidy levels. In this work, we focused on constructing a pan-genome of Eragrostis curvula to detect genomic variation,establish phylogenetic relationships, and analyze the effects of ploidy in genome evolution and reproductivemode. To do that, we used the genome assembly of cv. Victoria and genomic data, obtained by Illumina reads,of nine genetically diverse accessions of E. curvula. The construction of the pan-genome employed an iterativemapping and assembly approach involving the mapping of reads from different genotypes to the referencegenome assembly. The mapped reads were used for variant calling, while the unmapped reads wereassembled into new genomic fragments to annotate genes absent in the reference genome. These newlyassembled sequences were subsequently integrated into the reference genome, and the process was repeatediteratively for other genotypes. When all the accessions were processed, the final pan-genome comprised thereference genome and the newly assembled sequences. This approach proved to be highly efficient forconstructing a pan-genome exploiting the reference genome and the assembly of genetically distantgenotypes of E. curvula. Ultimately, the genomic resources generated were employed to gain a comprehensiveunderstanding of the genetic mechanisms underlying apomixis and related processes.
publishDate 2023
dc.date.none.fl_str_mv 2023
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info:eu-repo/semantics/conferenceObject
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Book
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info:ar-repo/semantics/documentoDeConferencia
status_str publishedVersion
format conferenceObject
dc.identifier.none.fl_str_mv http://hdl.handle.net/11336/241146
Developing a Pan-Genome of the diplosporous grass Eragrostis curvula; IV International Congress on Apomixis; Rosario; Argentina; 2023; 31-31
CONICET Digital
CONICET
url http://hdl.handle.net/11336/241146
identifier_str_mv Developing a Pan-Genome of the diplosporous grass Eragrostis curvula; IV International Congress on Apomixis; Rosario; Argentina; 2023; 31-31
CONICET Digital
CONICET
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language eng
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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/pdf
application/pdf
dc.coverage.none.fl_str_mv Internacional
dc.publisher.none.fl_str_mv Committee Organisation of IV International Congress on Apomixis
publisher.none.fl_str_mv Committee Organisation of IV International Congress on Apomixis
dc.source.none.fl_str_mv reponame:CONICET Digital (CONICET)
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