A chromosome scale assembly of Eragrostis curvula genome identify a region linked to apomixis

Autores
Carballo, José; Zappacosta, Diego Carlos; Selva, Juan Pablo; Bellido, Andres; Cáccamo, Mario José; Albertini, Emidio; Echenique, Carmen Viviana
Año de publicación
2022
Idioma
inglés
Tipo de recurso
documento de conferencia
Estado
versión publicada
Descripción
Eragrostis curvula is a grass species that is being studied in order to identify the genes and genomic regions involved in apomixis, an asexual mode of reproduction that avoid meiosis (apomeiosis) and fertilization of the egg cell and develops an embryo by parthenogenesis. Transferring apomixis to economically important crops will revolutionize the agriculture as we know it today since it can fix the hybrid vigor for generations. The identification of genomic regions associated to this trait and its regulatory components is central to transfer apomixis to other crops. In this way, we already sequenced a sexual diploid genotype, however, more complex apomictic tetraploids are necessary to perform comparative analyses. The tetraploid genome of the apomictic genotype Don Walter (2n=4x=40, ~1200 Mb) was sequenced using a combination of technologies to obtain a chromosome scale assembly. We used 10x genomic reads that were assembled with supernova software. Then, 20x of nanopore long reads were added with DGB2OLC software. Finally, Omni-C, the latest proximity ligation technology was used for scaffolding. The assembly has 1,171 Mb distributed in 3037 scaffolds. The N50 was 96 Mb and the number of genes was 133,619. The completeness of the genome was assessed using the BUSCO software finding 96,6% of complete genes. Performing a syntenic analysis with the diploid assembly we could get fully covered the 10 basic chromosomes of E. curvula. Through this analyses we could find regions that are only present in the apomictic genotype. Interestingly, SNPs markers linked to apomixis and candidates genes previously identified were mapped on a single region, togheter with other genes related to reproduction. Since the genome is collapsed in 10 chromosomes we could not distinguish if this region is present in all the haplotypes. More nanopore reads will be added in order to obtain an haplotype resolved assembly.
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
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: Selva, Juan Pablo. 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 Biología, Bioquímica y Farmacia; Argentina
Fil: Bellido, Andres. 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: Cáccamo, Mario José. National Institute Of Agricultural Botany.; Reino Unido
Fil: Albertini, Emidio. Università di Perugia; Italia
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
26th International Conference on Sexual Plant Reproduction
Praga
República Checa
Institute of Experimental Botany
Materia
ERAGROSTIS CURVULA
APOMIXIS
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:11336/224198
Acceder
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network_name_str CONICET Digital (CONICET)
spelling A chromosome scale assembly of Eragrostis curvula genome identify a region linked to apomixisCarballo, JoséZappacosta, Diego CarlosSelva, Juan PabloBellido, AndresCáccamo, Mario JoséAlbertini, EmidioEchenique, Carmen VivianaERAGROSTIS CURVULAAPOMIXIShttps://purl.org/becyt/ford/4.4https://purl.org/becyt/ford/4Eragrostis curvula is a grass species that is being studied in order to identify the genes and genomic regions involved in apomixis, an asexual mode of reproduction that avoid meiosis (apomeiosis) and fertilization of the egg cell and develops an embryo by parthenogenesis. Transferring apomixis to economically important crops will revolutionize the agriculture as we know it today since it can fix the hybrid vigor for generations. The identification of genomic regions associated to this trait and its regulatory components is central to transfer apomixis to other crops. In this way, we already sequenced a sexual diploid genotype, however, more complex apomictic tetraploids are necessary to perform comparative analyses. The tetraploid genome of the apomictic genotype Don Walter (2n=4x=40, ~1200 Mb) was sequenced using a combination of technologies to obtain a chromosome scale assembly. We used 10x genomic reads that were assembled with supernova software. Then, 20x of nanopore long reads were added with DGB2OLC software. Finally, Omni-C, the latest proximity ligation technology was used for scaffolding. The assembly has 1,171 Mb distributed in 3037 scaffolds. The N50 was 96 Mb and the number of genes was 133,619. The completeness of the genome was assessed using the BUSCO software finding 96,6% of complete genes. Performing a syntenic analysis with the diploid assembly we could get fully covered the 10 basic chromosomes of E. curvula. Through this analyses we could find regions that are only present in the apomictic genotype. Interestingly, SNPs markers linked to apomixis and candidates genes previously identified were mapped on a single region, togheter with other genes related to reproduction. Since the genome is collapsed in 10 chromosomes we could not distinguish if this region is present in all the haplotypes. More nanopore reads will be added in order to obtain an haplotype resolved assembly.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; ArgentinaFil: 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: Selva, Juan Pablo. 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 Biología, Bioquímica y Farmacia; ArgentinaFil: Bellido, Andres. 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: Cáccamo, Mario José. National Institute Of Agricultural Botany.; Reino UnidoFil: Albertini, Emidio. Università di Perugia; ItaliaFil: 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; Argentina26th International Conference on Sexual Plant ReproductionPragaRepública ChecaInstitute of Experimental BotanyInstitute of Experimental Botany2022info:eu-repo/semantics/publishedVersioninfo:eu-repo/semantics/conferenceObjectConferenciaBookhttp://purl.org/coar/resource_type/c_5794info:ar-repo/semantics/documentoDeConferenciaapplication/pdfapplication/pdfapplication/pdfapplication/pdfhttp://hdl.handle.net/11336/224198A chromosome scale assembly of Eragrostis curvula genome identify a region linked to apomixis; 26th International Conference on Sexual Plant Reproduction; Praga; República Checa; 2022; 1-40CONICET DigitalCONICETenginfo:eu-repo/semantics/altIdentifier/url/https://www.prague2020.eu/resources/Abstract-Book_ICSPR_18.06.2022.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 Técnicas2025-10-15T15:33:20Zoai:ri.conicet.gov.ar:11336/224198instacron: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:34982025-10-15 15:33:20.536CONICET Digital (CONICET) - Consejo Nacional de Investigaciones Científicas y Técnicasfalse
dc.title.none.fl_str_mv A chromosome scale assembly of Eragrostis curvula genome identify a region linked to apomixis
title A chromosome scale assembly of Eragrostis curvula genome identify a region linked to apomixis
spellingShingle A chromosome scale assembly of Eragrostis curvula genome identify a region linked to apomixis
Carballo, José
ERAGROSTIS CURVULA
APOMIXIS
title_short A chromosome scale assembly of Eragrostis curvula genome identify a region linked to apomixis
title_full A chromosome scale assembly of Eragrostis curvula genome identify a region linked to apomixis
title_fullStr A chromosome scale assembly of Eragrostis curvula genome identify a region linked to apomixis
title_full_unstemmed A chromosome scale assembly of Eragrostis curvula genome identify a region linked to apomixis
title_sort A chromosome scale assembly of Eragrostis curvula genome identify a region linked to apomixis
dc.creator.none.fl_str_mv Carballo, José
Zappacosta, Diego Carlos
Selva, Juan Pablo
Bellido, Andres
Cáccamo, Mario José
Albertini, Emidio
Echenique, Carmen Viviana
author Carballo, José
author_facet Carballo, José
Zappacosta, Diego Carlos
Selva, Juan Pablo
Bellido, Andres
Cáccamo, Mario José
Albertini, Emidio
Echenique, Carmen Viviana
author_role author
author2 Zappacosta, Diego Carlos
Selva, Juan Pablo
Bellido, Andres
Cáccamo, Mario José
Albertini, Emidio
Echenique, Carmen Viviana
author2_role author
author
author
author
author
author
dc.subject.none.fl_str_mv ERAGROSTIS CURVULA
APOMIXIS
topic ERAGROSTIS CURVULA
APOMIXIS
purl_subject.fl_str_mv https://purl.org/becyt/ford/4.4
https://purl.org/becyt/ford/4
dc.description.none.fl_txt_mv Eragrostis curvula is a grass species that is being studied in order to identify the genes and genomic regions involved in apomixis, an asexual mode of reproduction that avoid meiosis (apomeiosis) and fertilization of the egg cell and develops an embryo by parthenogenesis. Transferring apomixis to economically important crops will revolutionize the agriculture as we know it today since it can fix the hybrid vigor for generations. The identification of genomic regions associated to this trait and its regulatory components is central to transfer apomixis to other crops. In this way, we already sequenced a sexual diploid genotype, however, more complex apomictic tetraploids are necessary to perform comparative analyses. The tetraploid genome of the apomictic genotype Don Walter (2n=4x=40, ~1200 Mb) was sequenced using a combination of technologies to obtain a chromosome scale assembly. We used 10x genomic reads that were assembled with supernova software. Then, 20x of nanopore long reads were added with DGB2OLC software. Finally, Omni-C, the latest proximity ligation technology was used for scaffolding. The assembly has 1,171 Mb distributed in 3037 scaffolds. The N50 was 96 Mb and the number of genes was 133,619. The completeness of the genome was assessed using the BUSCO software finding 96,6% of complete genes. Performing a syntenic analysis with the diploid assembly we could get fully covered the 10 basic chromosomes of E. curvula. Through this analyses we could find regions that are only present in the apomictic genotype. Interestingly, SNPs markers linked to apomixis and candidates genes previously identified were mapped on a single region, togheter with other genes related to reproduction. Since the genome is collapsed in 10 chromosomes we could not distinguish if this region is present in all the haplotypes. More nanopore reads will be added in order to obtain an haplotype resolved assembly.
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
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: Selva, Juan Pablo. 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 Biología, Bioquímica y Farmacia; Argentina
Fil: Bellido, Andres. 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: Cáccamo, Mario José. National Institute Of Agricultural Botany.; Reino Unido
Fil: Albertini, Emidio. Università di Perugia; Italia
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
26th International Conference on Sexual Plant Reproduction
Praga
República Checa
Institute of Experimental Botany
description Eragrostis curvula is a grass species that is being studied in order to identify the genes and genomic regions involved in apomixis, an asexual mode of reproduction that avoid meiosis (apomeiosis) and fertilization of the egg cell and develops an embryo by parthenogenesis. Transferring apomixis to economically important crops will revolutionize the agriculture as we know it today since it can fix the hybrid vigor for generations. The identification of genomic regions associated to this trait and its regulatory components is central to transfer apomixis to other crops. In this way, we already sequenced a sexual diploid genotype, however, more complex apomictic tetraploids are necessary to perform comparative analyses. The tetraploid genome of the apomictic genotype Don Walter (2n=4x=40, ~1200 Mb) was sequenced using a combination of technologies to obtain a chromosome scale assembly. We used 10x genomic reads that were assembled with supernova software. Then, 20x of nanopore long reads were added with DGB2OLC software. Finally, Omni-C, the latest proximity ligation technology was used for scaffolding. The assembly has 1,171 Mb distributed in 3037 scaffolds. The N50 was 96 Mb and the number of genes was 133,619. The completeness of the genome was assessed using the BUSCO software finding 96,6% of complete genes. Performing a syntenic analysis with the diploid assembly we could get fully covered the 10 basic chromosomes of E. curvula. Through this analyses we could find regions that are only present in the apomictic genotype. Interestingly, SNPs markers linked to apomixis and candidates genes previously identified were mapped on a single region, togheter with other genes related to reproduction. Since the genome is collapsed in 10 chromosomes we could not distinguish if this region is present in all the haplotypes. More nanopore reads will be added in order to obtain an haplotype resolved assembly.
publishDate 2022
dc.date.none.fl_str_mv 2022
dc.type.none.fl_str_mv info:eu-repo/semantics/publishedVersion
info:eu-repo/semantics/conferenceObject
Conferencia
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/11336/224198
A chromosome scale assembly of Eragrostis curvula genome identify a region linked to apomixis; 26th International Conference on Sexual Plant Reproduction; Praga; República Checa; 2022; 1-40
CONICET Digital
CONICET
url http://hdl.handle.net/11336/224198
identifier_str_mv A chromosome scale assembly of Eragrostis curvula genome identify a region linked to apomixis; 26th International Conference on Sexual Plant Reproduction; Praga; República Checa; 2022; 1-40
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://www.prague2020.eu/resources/Abstract-Book_ICSPR_18.06.2022.pdf
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/pdf
application/pdf
application/pdf
dc.coverage.none.fl_str_mv Internacional
dc.publisher.none.fl_str_mv Institute of Experimental Botany
publisher.none.fl_str_mv Institute of Experimental Botany
dc.source.none.fl_str_mv reponame:CONICET Digital (CONICET)
instname:Consejo Nacional de Investigaciones Científicas y Técnicas
reponame_str CONICET Digital (CONICET)
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repository.mail.fl_str_mv dasensio@conicet.gov.ar; lcarlino@conicet.gov.ar
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