A completely phased diploid genome assembly for "Malbec" cultivar (Vitis vinifera L.)

Autores
Calderón, Pablo Luciano Sebastian; Carbonell Bejerano, P.; Mauri, N; Muñoz, Claudio Javier; Bree, Laura; Sola, C; Bergamin, D; Gómez Talquenca, Sebastián; Ibañez, J; Martinez-Zapater, JM; Lijavetzky, Diego Claudio
Año de publicación
2021
Idioma
inglés
Tipo de recurso
documento de conferencia
Estado
versión publicada
Descripción
Most grapevine cultivars originated from the outcrossing of two genetically diverse parents, and are clonally propagated to preserve phenotypes of productive interest. Hence, cultivars are first filial generations (F1) with highly heterozygous diploid genomes, that turn challenging to assemble. "Malbec" is the main cultivar for the Argentine wine industry and it originated in France, from the outcrossing of Magdeleine Noir des Charentes and Prunelard cultivars. Based on that mother-father-offspring relationship, here we followed the algorithm implemented in the software CanuTrio to produce a phased assembly of Malbec genome. For this aim, parental cultivars? Illumina short-reads were used to sort ?Malbec? PacBio long-reads into its haploid complements, to be assembled separately. Post- assembly, bioinformatic procedures were employed to reduce the number of duplicated regions and perform sequence error corrections (using Malbec Illumina short-reads). We obtained two highly complete and contiguous haploid assemblies for Malbec, Haplotype- Prunelard (482.4 Mb size; contig N50=7.7 Mb) and Haplotype-Magdeleine (479.4 Mb size; contig N50=6.6 Mb), with 96.1 and 95.8% of BUSCO genes, respectively. We tested for the composition of both haplophases with the tool Merqury, and observed <0.13% of haplotype switches, meaning that Malbec genomic information was correctly assigned to each haploid assembly. Finally, a variant calling analysis indicated a great diversity between Malbec haplophases, with >15% of both assemblies affected by structural variations, along with 3.2 million SNPs and 0.6 million InDels. Our results indicate that this is a valid approach to assemble highly heterozygous and complex diploid genomes in a completely-phased way.
Fil: Calderón, Pablo Luciano Sebastian. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Mendoza. Instituto de Biología Agrícola de Mendoza. Universidad Nacional de Cuyo. Facultad de Ciencias Agrarias. Instituto de Biología Agrícola de Mendoza; Argentina
Fil: Carbonell Bejerano, P.. Max Planck Institute for Developmental Biology; Alemania
Fil: Mauri, N. Instituto de Ciencias de la Vid y del Vino; España
Fil: Muñoz, Claudio Javier. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Mendoza. Instituto de Biología Agrícola de Mendoza. Universidad Nacional de Cuyo. Facultad de Ciencias Agrarias. Instituto de Biología Agrícola de Mendoza; Argentina
Fil: Bree, Laura. No especifíca;
Fil: Sola, C. No especifíca;
Fil: Bergamin, D. No especifíca;
Fil: Gómez Talquenca, Sebastián. Instituto Nacional de Tecnología Agropecuaria; Argentina
Fil: Ibañez, J. Instituto de Ciencias de la Vid y del Vino; España
Fil: Martinez-Zapater, JM. Instituto de Ciencias de la Vid y del Vino; España
Fil: Lijavetzky, Diego Claudio. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Mendoza. Instituto de Biología Agrícola de Mendoza. Universidad Nacional de Cuyo. Facultad de Ciencias Agrarias. Instituto de Biología Agrícola de Mendoza; Argentina
XVIII Congreso Latinoamericano de Genética; LIV Reunión Anual de la Sociedad de Genética de Chile; XLIX Congreso Argentino de Genética; VIII Congreso de la Sociedad Uruguaya de Genética; I Congreso Paraguayo de Genética y V Congreso Latinoamericano de Genética Humana
Chile
Sociedad Argentina de Genética
Materia
Malbec
Genome Assambly
PacBio
Illumina
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:11336/167676
Acceder
id CONICETDig_10554935d40c633386bcf0da1a85fc9f
oai_identifier_str oai:ri.conicet.gov.ar:11336/167676
network_acronym_str CONICETDig
repository_id_str 3498
network_name_str CONICET Digital (CONICET)
spelling A completely phased diploid genome assembly for "Malbec" cultivar (Vitis vinifera L.)Calderón, Pablo Luciano SebastianCarbonell Bejerano, P.Mauri, NMuñoz, Claudio JavierBree, LauraSola, CBergamin, DGómez Talquenca, SebastiánIbañez, JMartinez-Zapater, JMLijavetzky, Diego ClaudioMalbecGenome AssamblyPacBioIlluminahttps://purl.org/becyt/ford/1.6https://purl.org/becyt/ford/1Most grapevine cultivars originated from the outcrossing of two genetically diverse parents, and are clonally propagated to preserve phenotypes of productive interest. Hence, cultivars are first filial generations (F1) with highly heterozygous diploid genomes, that turn challenging to assemble. "Malbec" is the main cultivar for the Argentine wine industry and it originated in France, from the outcrossing of Magdeleine Noir des Charentes and Prunelard cultivars. Based on that mother-father-offspring relationship, here we followed the algorithm implemented in the software CanuTrio to produce a phased assembly of Malbec genome. For this aim, parental cultivars? Illumina short-reads were used to sort ?Malbec? PacBio long-reads into its haploid complements, to be assembled separately. Post- assembly, bioinformatic procedures were employed to reduce the number of duplicated regions and perform sequence error corrections (using Malbec Illumina short-reads). We obtained two highly complete and contiguous haploid assemblies for Malbec, Haplotype- Prunelard (482.4 Mb size; contig N50=7.7 Mb) and Haplotype-Magdeleine (479.4 Mb size; contig N50=6.6 Mb), with 96.1 and 95.8% of BUSCO genes, respectively. We tested for the composition of both haplophases with the tool Merqury, and observed <0.13% of haplotype switches, meaning that Malbec genomic information was correctly assigned to each haploid assembly. Finally, a variant calling analysis indicated a great diversity between Malbec haplophases, with >15% of both assemblies affected by structural variations, along with 3.2 million SNPs and 0.6 million InDels. Our results indicate that this is a valid approach to assemble highly heterozygous and complex diploid genomes in a completely-phased way.Fil: Calderón, Pablo Luciano Sebastian. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Mendoza. Instituto de Biología Agrícola de Mendoza. Universidad Nacional de Cuyo. Facultad de Ciencias Agrarias. Instituto de Biología Agrícola de Mendoza; ArgentinaFil: Carbonell Bejerano, P.. Max Planck Institute for Developmental Biology; AlemaniaFil: Mauri, N. Instituto de Ciencias de la Vid y del Vino; EspañaFil: Muñoz, Claudio Javier. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Mendoza. Instituto de Biología Agrícola de Mendoza. Universidad Nacional de Cuyo. Facultad de Ciencias Agrarias. Instituto de Biología Agrícola de Mendoza; ArgentinaFil: Bree, Laura. No especifíca;Fil: Sola, C. No especifíca;Fil: Bergamin, D. No especifíca;Fil: Gómez Talquenca, Sebastián. Instituto Nacional de Tecnología Agropecuaria; ArgentinaFil: Ibañez, J. Instituto de Ciencias de la Vid y del Vino; EspañaFil: Martinez-Zapater, JM. Instituto de Ciencias de la Vid y del Vino; EspañaFil: Lijavetzky, Diego Claudio. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Mendoza. Instituto de Biología Agrícola de Mendoza. Universidad Nacional de Cuyo. Facultad de Ciencias Agrarias. Instituto de Biología Agrícola de Mendoza; ArgentinaXVIII Congreso Latinoamericano de Genética; LIV Reunión Anual de la Sociedad de Genética de Chile; XLIX Congreso Argentino de Genética; VIII Congreso de la Sociedad Uruguaya de Genética; I Congreso Paraguayo de Genética y V Congreso Latinoamericano de Genética HumanaChileSociedad Argentina de GenéticaSociedad Argentina de Genética2021info:eu-repo/semantics/publishedVersioninfo:eu-repo/semantics/conferenceObjectCongresoJournalhttp://purl.org/coar/resource_type/c_5794info:ar-repo/semantics/documentoDeConferenciaapplication/pdfapplication/pdfapplication/pdfhttp://hdl.handle.net/11336/167676A completely phased diploid genome assembly for "Malbec" cultivar (Vitis vinifera L.); XVIII Congreso Latinoamericano de Genética; LIV Reunión Anual de la Sociedad de Genética de Chile; XLIX Congreso Argentino de Genética; VIII Congreso de la Sociedad Uruguaya de Genética; I Congreso Paraguayo de Genética y V Congreso Latinoamericano de Genética Humana; Chile; 2021; 1-21852-6322CONICET DigitalCONICETenginfo:eu-repo/semantics/altIdentifier/url/https://sag.org.ar/jbag/project/vol-xxxii-suppl-1/info:eu-repo/semantics/altIdentifier/doi/10.35407/bag.2021.32.01.supplInternacionalinfo:eu-repo/semantics/openAccesshttps://creativecommons.org/licenses/by-nc-sa/2.5/ar/reponame:CONICET Digital (CONICET)instname:Consejo Nacional de Investigaciones Científicas y Técnicas2025-09-29T09:44:25Zoai:ri.conicet.gov.ar:11336/167676instacron: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 09:44:25.803CONICET Digital (CONICET) - Consejo Nacional de Investigaciones Científicas y Técnicasfalse
dc.title.none.fl_str_mv A completely phased diploid genome assembly for "Malbec" cultivar (Vitis vinifera L.)
title A completely phased diploid genome assembly for "Malbec" cultivar (Vitis vinifera L.)
spellingShingle A completely phased diploid genome assembly for "Malbec" cultivar (Vitis vinifera L.)
Calderón, Pablo Luciano Sebastian
Malbec
Genome Assambly
PacBio
Illumina
title_short A completely phased diploid genome assembly for "Malbec" cultivar (Vitis vinifera L.)
title_full A completely phased diploid genome assembly for "Malbec" cultivar (Vitis vinifera L.)
title_fullStr A completely phased diploid genome assembly for "Malbec" cultivar (Vitis vinifera L.)
title_full_unstemmed A completely phased diploid genome assembly for "Malbec" cultivar (Vitis vinifera L.)
title_sort A completely phased diploid genome assembly for "Malbec" cultivar (Vitis vinifera L.)
dc.creator.none.fl_str_mv Calderón, Pablo Luciano Sebastian
Carbonell Bejerano, P.
Mauri, N
Muñoz, Claudio Javier
Bree, Laura
Sola, C
Bergamin, D
Gómez Talquenca, Sebastián
Ibañez, J
Martinez-Zapater, JM
Lijavetzky, Diego Claudio
author Calderón, Pablo Luciano Sebastian
author_facet Calderón, Pablo Luciano Sebastian
Carbonell Bejerano, P.
Mauri, N
Muñoz, Claudio Javier
Bree, Laura
Sola, C
Bergamin, D
Gómez Talquenca, Sebastián
Ibañez, J
Martinez-Zapater, JM
Lijavetzky, Diego Claudio
author_role author
author2 Carbonell Bejerano, P.
Mauri, N
Muñoz, Claudio Javier
Bree, Laura
Sola, C
Bergamin, D
Gómez Talquenca, Sebastián
Ibañez, J
Martinez-Zapater, JM
Lijavetzky, Diego Claudio
author2_role author
author
author
author
author
author
author
author
author
author
dc.subject.none.fl_str_mv Malbec
Genome Assambly
PacBio
Illumina
topic Malbec
Genome Assambly
PacBio
Illumina
purl_subject.fl_str_mv https://purl.org/becyt/ford/1.6
https://purl.org/becyt/ford/1
dc.description.none.fl_txt_mv Most grapevine cultivars originated from the outcrossing of two genetically diverse parents, and are clonally propagated to preserve phenotypes of productive interest. Hence, cultivars are first filial generations (F1) with highly heterozygous diploid genomes, that turn challenging to assemble. "Malbec" is the main cultivar for the Argentine wine industry and it originated in France, from the outcrossing of Magdeleine Noir des Charentes and Prunelard cultivars. Based on that mother-father-offspring relationship, here we followed the algorithm implemented in the software CanuTrio to produce a phased assembly of Malbec genome. For this aim, parental cultivars? Illumina short-reads were used to sort ?Malbec? PacBio long-reads into its haploid complements, to be assembled separately. Post- assembly, bioinformatic procedures were employed to reduce the number of duplicated regions and perform sequence error corrections (using Malbec Illumina short-reads). We obtained two highly complete and contiguous haploid assemblies for Malbec, Haplotype- Prunelard (482.4 Mb size; contig N50=7.7 Mb) and Haplotype-Magdeleine (479.4 Mb size; contig N50=6.6 Mb), with 96.1 and 95.8% of BUSCO genes, respectively. We tested for the composition of both haplophases with the tool Merqury, and observed <0.13% of haplotype switches, meaning that Malbec genomic information was correctly assigned to each haploid assembly. Finally, a variant calling analysis indicated a great diversity between Malbec haplophases, with >15% of both assemblies affected by structural variations, along with 3.2 million SNPs and 0.6 million InDels. Our results indicate that this is a valid approach to assemble highly heterozygous and complex diploid genomes in a completely-phased way.
Fil: Calderón, Pablo Luciano Sebastian. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Mendoza. Instituto de Biología Agrícola de Mendoza. Universidad Nacional de Cuyo. Facultad de Ciencias Agrarias. Instituto de Biología Agrícola de Mendoza; Argentina
Fil: Carbonell Bejerano, P.. Max Planck Institute for Developmental Biology; Alemania
Fil: Mauri, N. Instituto de Ciencias de la Vid y del Vino; España
Fil: Muñoz, Claudio Javier. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Mendoza. Instituto de Biología Agrícola de Mendoza. Universidad Nacional de Cuyo. Facultad de Ciencias Agrarias. Instituto de Biología Agrícola de Mendoza; Argentina
Fil: Bree, Laura. No especifíca;
Fil: Sola, C. No especifíca;
Fil: Bergamin, D. No especifíca;
Fil: Gómez Talquenca, Sebastián. Instituto Nacional de Tecnología Agropecuaria; Argentina
Fil: Ibañez, J. Instituto de Ciencias de la Vid y del Vino; España
Fil: Martinez-Zapater, JM. Instituto de Ciencias de la Vid y del Vino; España
Fil: Lijavetzky, Diego Claudio. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Mendoza. Instituto de Biología Agrícola de Mendoza. Universidad Nacional de Cuyo. Facultad de Ciencias Agrarias. Instituto de Biología Agrícola de Mendoza; Argentina
XVIII Congreso Latinoamericano de Genética; LIV Reunión Anual de la Sociedad de Genética de Chile; XLIX Congreso Argentino de Genética; VIII Congreso de la Sociedad Uruguaya de Genética; I Congreso Paraguayo de Genética y V Congreso Latinoamericano de Genética Humana
Chile
Sociedad Argentina de Genética
description Most grapevine cultivars originated from the outcrossing of two genetically diverse parents, and are clonally propagated to preserve phenotypes of productive interest. Hence, cultivars are first filial generations (F1) with highly heterozygous diploid genomes, that turn challenging to assemble. "Malbec" is the main cultivar for the Argentine wine industry and it originated in France, from the outcrossing of Magdeleine Noir des Charentes and Prunelard cultivars. Based on that mother-father-offspring relationship, here we followed the algorithm implemented in the software CanuTrio to produce a phased assembly of Malbec genome. For this aim, parental cultivars? Illumina short-reads were used to sort ?Malbec? PacBio long-reads into its haploid complements, to be assembled separately. Post- assembly, bioinformatic procedures were employed to reduce the number of duplicated regions and perform sequence error corrections (using Malbec Illumina short-reads). We obtained two highly complete and contiguous haploid assemblies for Malbec, Haplotype- Prunelard (482.4 Mb size; contig N50=7.7 Mb) and Haplotype-Magdeleine (479.4 Mb size; contig N50=6.6 Mb), with 96.1 and 95.8% of BUSCO genes, respectively. We tested for the composition of both haplophases with the tool Merqury, and observed <0.13% of haplotype switches, meaning that Malbec genomic information was correctly assigned to each haploid assembly. Finally, a variant calling analysis indicated a great diversity between Malbec haplophases, with >15% of both assemblies affected by structural variations, along with 3.2 million SNPs and 0.6 million InDels. Our results indicate that this is a valid approach to assemble highly heterozygous and complex diploid genomes in a completely-phased way.
publishDate 2021
dc.date.none.fl_str_mv 2021
dc.type.none.fl_str_mv info:eu-repo/semantics/publishedVersion
info:eu-repo/semantics/conferenceObject
Congreso
Journal
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/11336/167676
A completely phased diploid genome assembly for "Malbec" cultivar (Vitis vinifera L.); XVIII Congreso Latinoamericano de Genética; LIV Reunión Anual de la Sociedad de Genética de Chile; XLIX Congreso Argentino de Genética; VIII Congreso de la Sociedad Uruguaya de Genética; I Congreso Paraguayo de Genética y V Congreso Latinoamericano de Genética Humana; Chile; 2021; 1-2
1852-6322
CONICET Digital
CONICET
url http://hdl.handle.net/11336/167676
identifier_str_mv A completely phased diploid genome assembly for "Malbec" cultivar (Vitis vinifera L.); XVIII Congreso Latinoamericano de Genética; LIV Reunión Anual de la Sociedad de Genética de Chile; XLIX Congreso Argentino de Genética; VIII Congreso de la Sociedad Uruguaya de Genética; I Congreso Paraguayo de Genética y V Congreso Latinoamericano de Genética Humana; Chile; 2021; 1-2
1852-6322
CONICET Digital
CONICET
dc.language.none.fl_str_mv eng
language eng
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info:eu-repo/semantics/altIdentifier/doi/10.35407/bag.2021.32.01.suppl
dc.rights.none.fl_str_mv info:eu-repo/semantics/openAccess
https://creativecommons.org/licenses/by-nc-sa/2.5/ar/
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application/pdf
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dc.coverage.none.fl_str_mv Internacional
dc.publisher.none.fl_str_mv Sociedad Argentina de Genética
publisher.none.fl_str_mv Sociedad Argentina de Genética
dc.source.none.fl_str_mv reponame:CONICET Digital (CONICET)
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instname_str Consejo Nacional de Investigaciones Científicas y Técnicas
repository.name.fl_str_mv CONICET Digital (CONICET) - Consejo Nacional de Investigaciones Científicas y Técnicas
repository.mail.fl_str_mv dasensio@conicet.gov.ar; lcarlino@conicet.gov.ar
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