A Genomic Approach to Study Apomixis using Eragrostis curvula as a Model Species

Autores
Carballo, José; Garbus, Ingrid; Selva, Juan Pablo; Santos, Bruno A.; Albertini, Emidio; Cáccamo, Mario José; Echenique, Carmen Viviana
Año de publicación
2018
Idioma
inglés
Tipo de recurso
documento de conferencia
Estado
versión publicada
Descripción
Apomixis is defined as asexual reproduction by seeds, avoiding meiotic reduction and fertilization, being generally present in polyploid plant species. Eragrostis curvula is a perennial grass native to Southern Africa. This species can be taken as a model for the discovery of genes that govern pseudogamous diplosporic apomixis since its polyploid cytotypes (4x to 8x) may undergo sexual reproduction, facultative apomixis, or obligate apomixis whereas diploids are always sexual. Here we present the first draft of a diploid version of the E. curvula genome. The cultivar selected was Victoria (~1200 Mb) originated from in vitro culture of inflorescences of the apomictic cv. Tanganyika (2n=4x=40). Two libraries were prepared with fragment lengths of 20 kb and 10 kb to get longer reads and to increase the coverage, respectively. The sequencing through PACBIO technology resulted in 6.223.627 and 3.309.811 reads respectively with 90X coverage. The assembly was performed using the software Falcon. The N50 was 380.026 bp with 3.118 contigs representing 95% of the haplotype length. The software BUSCO was used to find single copy orthologous genes, being represented 97% of the BUSCO genes. Dovetail Hi-rise software revealed the architecture of the complete genome chromosome-by-chromosome. The first draft of E. curvula genome showed high level of contiguity with a coverage of 95% of the diploid genome. The high proportion of annotated genes would allow the identification of those related to the reproductive mode. This draft represents the start point to obtain more complex tetraploid genomes, harboring the region/s involved in apomixis.
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: Garbus, Ingrid. 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: 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
Fil: Santos, Bruno A.. National Institute of Agricultural Botany; Reino Unido
Fil: Albertini, Emidio. Università di Perugia; Italia
Fil: Cáccamo, Mario José. National Institute of Agricultural Botany; Reino Unido
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
Plant and Animal Genome XXVI Conference (PAG)
San Diego
Estados Unidos
Plant and Animal Genome
Materia
GENOME
PACBIO
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:11336/225696
Acceder
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oai_identifier_str oai:ri.conicet.gov.ar:11336/225696
network_acronym_str CONICETDig
repository_id_str 3498
network_name_str CONICET Digital (CONICET)
spelling A Genomic Approach to Study Apomixis using Eragrostis curvula as a Model SpeciesCarballo, JoséGarbus, IngridSelva, Juan PabloSantos, Bruno A.Albertini, EmidioCáccamo, Mario JoséEchenique, Carmen VivianaGENOMEPACBIOERAGROSTIS CURVULAAPOMIXIShttps://purl.org/becyt/ford/1.6https://purl.org/becyt/ford/1Apomixis is defined as asexual reproduction by seeds, avoiding meiotic reduction and fertilization, being generally present in polyploid plant species. Eragrostis curvula is a perennial grass native to Southern Africa. This species can be taken as a model for the discovery of genes that govern pseudogamous diplosporic apomixis since its polyploid cytotypes (4x to 8x) may undergo sexual reproduction, facultative apomixis, or obligate apomixis whereas diploids are always sexual. Here we present the first draft of a diploid version of the E. curvula genome. The cultivar selected was Victoria (~1200 Mb) originated from in vitro culture of inflorescences of the apomictic cv. Tanganyika (2n=4x=40). Two libraries were prepared with fragment lengths of 20 kb and 10 kb to get longer reads and to increase the coverage, respectively. The sequencing through PACBIO technology resulted in 6.223.627 and 3.309.811 reads respectively with 90X coverage. The assembly was performed using the software Falcon. The N50 was 380.026 bp with 3.118 contigs representing 95% of the haplotype length. The software BUSCO was used to find single copy orthologous genes, being represented 97% of the BUSCO genes. Dovetail Hi-rise software revealed the architecture of the complete genome chromosome-by-chromosome. The first draft of E. curvula genome showed high level of contiguity with a coverage of 95% of the diploid genome. The high proportion of annotated genes would allow the identification of those related to the reproductive mode. This draft represents the start point to obtain more complex tetraploid genomes, harboring the region/s involved in apomixis.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: Garbus, Ingrid. 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: 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; ArgentinaFil: Santos, Bruno A.. National Institute of Agricultural Botany; Reino UnidoFil: Albertini, Emidio. Università di Perugia; ItaliaFil: Cáccamo, Mario José. National Institute of Agricultural Botany; Reino UnidoFil: 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; ArgentinaPlant and Animal Genome XXVI Conference (PAG)San DiegoEstados UnidosPlant and Animal GenomePlant and Animal Genome2018info: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/11336/225696A Genomic Approach to Study Apomixis using Eragrostis curvula as a Model Species; Plant and Animal Genome XXVI Conference (PAG); San Diego; Estados Unidos; 2018; 1-1CONICET DigitalCONICETenginfo:eu-repo/semantics/altIdentifier/url/http://www.intlpag.orginfo:eu-repo/semantics/altIdentifier/url/https://plan.core-apps.com/pag_2018/abstract/ea4431cd14b6570e9d2f2a543c201bc4Internacionalinfo:eu-repo/semantics/openAccesshttps://creativecommons.org/licenses/by-nc-sa/2.5/ar/reponame:CONICET Digital (CONICET)instname:Consejo Nacional de Investigaciones Científicas y Técnicas2025-10-15T14:51:50Zoai:ri.conicet.gov.ar:11336/225696instacron: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 14:51:50.706CONICET Digital (CONICET) - Consejo Nacional de Investigaciones Científicas y Técnicasfalse
dc.title.none.fl_str_mv A Genomic Approach to Study Apomixis using Eragrostis curvula as a Model Species
title A Genomic Approach to Study Apomixis using Eragrostis curvula as a Model Species
spellingShingle A Genomic Approach to Study Apomixis using Eragrostis curvula as a Model Species
Carballo, José
GENOME
PACBIO
ERAGROSTIS CURVULA
APOMIXIS
title_short A Genomic Approach to Study Apomixis using Eragrostis curvula as a Model Species
title_full A Genomic Approach to Study Apomixis using Eragrostis curvula as a Model Species
title_fullStr A Genomic Approach to Study Apomixis using Eragrostis curvula as a Model Species
title_full_unstemmed A Genomic Approach to Study Apomixis using Eragrostis curvula as a Model Species
title_sort A Genomic Approach to Study Apomixis using Eragrostis curvula as a Model Species
dc.creator.none.fl_str_mv Carballo, José
Garbus, Ingrid
Selva, Juan Pablo
Santos, Bruno A.
Albertini, Emidio
Cáccamo, Mario José
Echenique, Carmen Viviana
author Carballo, José
author_facet Carballo, José
Garbus, Ingrid
Selva, Juan Pablo
Santos, Bruno A.
Albertini, Emidio
Cáccamo, Mario José
Echenique, Carmen Viviana
author_role author
author2 Garbus, Ingrid
Selva, Juan Pablo
Santos, Bruno A.
Albertini, Emidio
Cáccamo, Mario José
Echenique, Carmen Viviana
author2_role author
author
author
author
author
author
dc.subject.none.fl_str_mv GENOME
PACBIO
ERAGROSTIS CURVULA
APOMIXIS
topic GENOME
PACBIO
ERAGROSTIS CURVULA
APOMIXIS
purl_subject.fl_str_mv https://purl.org/becyt/ford/1.6
https://purl.org/becyt/ford/1
dc.description.none.fl_txt_mv Apomixis is defined as asexual reproduction by seeds, avoiding meiotic reduction and fertilization, being generally present in polyploid plant species. Eragrostis curvula is a perennial grass native to Southern Africa. This species can be taken as a model for the discovery of genes that govern pseudogamous diplosporic apomixis since its polyploid cytotypes (4x to 8x) may undergo sexual reproduction, facultative apomixis, or obligate apomixis whereas diploids are always sexual. Here we present the first draft of a diploid version of the E. curvula genome. The cultivar selected was Victoria (~1200 Mb) originated from in vitro culture of inflorescences of the apomictic cv. Tanganyika (2n=4x=40). Two libraries were prepared with fragment lengths of 20 kb and 10 kb to get longer reads and to increase the coverage, respectively. The sequencing through PACBIO technology resulted in 6.223.627 and 3.309.811 reads respectively with 90X coverage. The assembly was performed using the software Falcon. The N50 was 380.026 bp with 3.118 contigs representing 95% of the haplotype length. The software BUSCO was used to find single copy orthologous genes, being represented 97% of the BUSCO genes. Dovetail Hi-rise software revealed the architecture of the complete genome chromosome-by-chromosome. The first draft of E. curvula genome showed high level of contiguity with a coverage of 95% of the diploid genome. The high proportion of annotated genes would allow the identification of those related to the reproductive mode. This draft represents the start point to obtain more complex tetraploid genomes, harboring the region/s involved in apomixis.
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: Garbus, Ingrid. 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: 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
Fil: Santos, Bruno A.. National Institute of Agricultural Botany; Reino Unido
Fil: Albertini, Emidio. Università di Perugia; Italia
Fil: Cáccamo, Mario José. National Institute of Agricultural Botany; Reino Unido
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
Plant and Animal Genome XXVI Conference (PAG)
San Diego
Estados Unidos
Plant and Animal Genome
description Apomixis is defined as asexual reproduction by seeds, avoiding meiotic reduction and fertilization, being generally present in polyploid plant species. Eragrostis curvula is a perennial grass native to Southern Africa. This species can be taken as a model for the discovery of genes that govern pseudogamous diplosporic apomixis since its polyploid cytotypes (4x to 8x) may undergo sexual reproduction, facultative apomixis, or obligate apomixis whereas diploids are always sexual. Here we present the first draft of a diploid version of the E. curvula genome. The cultivar selected was Victoria (~1200 Mb) originated from in vitro culture of inflorescences of the apomictic cv. Tanganyika (2n=4x=40). Two libraries were prepared with fragment lengths of 20 kb and 10 kb to get longer reads and to increase the coverage, respectively. The sequencing through PACBIO technology resulted in 6.223.627 and 3.309.811 reads respectively with 90X coverage. The assembly was performed using the software Falcon. The N50 was 380.026 bp with 3.118 contigs representing 95% of the haplotype length. The software BUSCO was used to find single copy orthologous genes, being represented 97% of the BUSCO genes. Dovetail Hi-rise software revealed the architecture of the complete genome chromosome-by-chromosome. The first draft of E. curvula genome showed high level of contiguity with a coverage of 95% of the diploid genome. The high proportion of annotated genes would allow the identification of those related to the reproductive mode. This draft represents the start point to obtain more complex tetraploid genomes, harboring the region/s involved in apomixis.
publishDate 2018
dc.date.none.fl_str_mv 2018
dc.type.none.fl_str_mv info:eu-repo/semantics/publishedVersion
info:eu-repo/semantics/conferenceObject
Congreso
Book
http://purl.org/coar/resource_type/c_5794
info:ar-repo/semantics/documentoDeConferencia
status_str publishedVersion
format conferenceObject
dc.identifier.none.fl_str_mv http://hdl.handle.net/11336/225696
A Genomic Approach to Study Apomixis using Eragrostis curvula as a Model Species; Plant and Animal Genome XXVI Conference (PAG); San Diego; Estados Unidos; 2018; 1-1
CONICET Digital
CONICET
url http://hdl.handle.net/11336/225696
identifier_str_mv A Genomic Approach to Study Apomixis using Eragrostis curvula as a Model Species; Plant and Animal Genome XXVI Conference (PAG); San Diego; Estados Unidos; 2018; 1-1
CONICET Digital
CONICET
dc.language.none.fl_str_mv eng
language eng
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application/pdf
application/pdf
dc.coverage.none.fl_str_mv Internacional
dc.publisher.none.fl_str_mv Plant and Animal Genome
publisher.none.fl_str_mv Plant and Animal Genome
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repository.mail.fl_str_mv dasensio@conicet.gov.ar; lcarlino@conicet.gov.ar
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