Diploid genome assembly of the Malbec grapevine cultivar enables haplotype-aware analysis of transcriptomic differences underlying clonal phenotypic variation
- Autores
- Calderón, Pablo Luciano Sebastian; Carbonell Bejerano, Pablo; Muñoz, Claudio Javier; Bree, Laura; Sola, Cristobal; Bergamin, Daniel; Tulle, Walter Daniel; Gómez Talquenca, Sebastián; Lanz, Christa; Royo, Carolina; Ibañez, Javier; Martínez Zapater, José M.; Weigel, Detlef; Lijavetzky, Diego Claudio
- Año de publicación
- 2024
- Idioma
- inglés
- Tipo de recurso
- artículo
- Estado
- versión publicada
- Descripción
- To preserve their varietal attributes established grapevine cultivars (Vitis vinifera L. ssp. vinifera) must be clonally propagated, due to their highly heterozygous genomes. Malbec is a France-originated cultivar appreciated for producing high-quality wines, and is the offspring of cultivars Prunelard and Magdeleine Noire des Charentes. Here, we have built a diploid genome assembly of Malbec, after trio binning of PacBio long reads into the two haploid complements inherited from either parent. After haplotype-aware deduplication and corrections, complete assemblies for the two haplophases were obtained with very low haplotype switch-error rate (<0.025). The haplophases alignment identified >25% of polymorphic regions. Gene annotation including RNA-seq transcriptome assembly and ab initio prediction evidence resulted in similar gene model numbers for both haplophases. The annotated diploid assembly was exploited in the transcriptomic comparison of four clonal accessions of Malbec that exhibited variation in berry composition traits. Analysis of the ripening pericarp transcriptome using either haplophases as reference yielded similar results, although some differences were observed. Particularly, among the differentially expressed genes identified only with the Magdeleine-inherited haplotype as reference, we observed an over-representation of hypothetically hemizygous genes. The higher berry anthocyanin content of clonal accession 595 was associated with increased abscisic acid responses, possibly leading to the observed overexpression of phenylpropanoid metabolism genes and deregulation of genes associated to abiotic stress response. Overall, the results highlight the importance of producing diploid assemblies to fully represent the genomic diversity of highly heterozygous woody crop cultivars and to unveil the molecular bases of clonal phenotypic variation.
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, Pablo. Instituto de Ciencias de la Vid y El Vino ; Consejo Superior de Investigaciones Cientificas;
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, Cristobal. No especifíca;
Fil: Bergamin, Daniel. No especifíca;
Fil: Tulle, Walter Daniel. 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: Gómez Talquenca, Sebastián. Instituto Nacional de Tecnología Agropecuaria; Argentina
Fil: Lanz, Christa. Max Planck Institute for Biology of Ageing; Alemania
Fil: Royo, Carolina. Universidad de La Rioja; España
Fil: Ibañez, Javier. Universidad de La Rioja; España
Fil: Martínez Zapater, José M.. Universidad de La Rioja; España
Fil: Weigel, Detlef. Max Planck Institute for Biology of Ageing; Alemania
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 - Materia
-
MALBEC GENOME
GRAPEVINE
VITIS
RNA-SEQ - Nivel de accesibilidad
- acceso abierto
- Condiciones de uso
- https://creativecommons.org/licenses/by-nc-sa/2.5/ar/
- Repositorio
- Institución
- Consejo Nacional de Investigaciones Científicas y Técnicas
- OAI Identificador
- oai:ri.conicet.gov.ar:11336/241295
Ver los metadatos del registro completo
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oai:ri.conicet.gov.ar:11336/241295 |
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CONICET Digital (CONICET) |
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Diploid genome assembly of the Malbec grapevine cultivar enables haplotype-aware analysis of transcriptomic differences underlying clonal phenotypic variationCalderón, Pablo Luciano SebastianCarbonell Bejerano, PabloMuñoz, Claudio JavierBree, LauraSola, CristobalBergamin, DanielTulle, Walter DanielGómez Talquenca, SebastiánLanz, ChristaRoyo, CarolinaIbañez, JavierMartínez Zapater, José M.Weigel, DetlefLijavetzky, Diego ClaudioMALBEC GENOMEGRAPEVINEVITISRNA-SEQhttps://purl.org/becyt/ford/1.6https://purl.org/becyt/ford/1To preserve their varietal attributes established grapevine cultivars (Vitis vinifera L. ssp. vinifera) must be clonally propagated, due to their highly heterozygous genomes. Malbec is a France-originated cultivar appreciated for producing high-quality wines, and is the offspring of cultivars Prunelard and Magdeleine Noire des Charentes. Here, we have built a diploid genome assembly of Malbec, after trio binning of PacBio long reads into the two haploid complements inherited from either parent. After haplotype-aware deduplication and corrections, complete assemblies for the two haplophases were obtained with very low haplotype switch-error rate (<0.025). The haplophases alignment identified >25% of polymorphic regions. Gene annotation including RNA-seq transcriptome assembly and ab initio prediction evidence resulted in similar gene model numbers for both haplophases. The annotated diploid assembly was exploited in the transcriptomic comparison of four clonal accessions of Malbec that exhibited variation in berry composition traits. Analysis of the ripening pericarp transcriptome using either haplophases as reference yielded similar results, although some differences were observed. Particularly, among the differentially expressed genes identified only with the Magdeleine-inherited haplotype as reference, we observed an over-representation of hypothetically hemizygous genes. The higher berry anthocyanin content of clonal accession 595 was associated with increased abscisic acid responses, possibly leading to the observed overexpression of phenylpropanoid metabolism genes and deregulation of genes associated to abiotic stress response. Overall, the results highlight the importance of producing diploid assemblies to fully represent the genomic diversity of highly heterozygous woody crop cultivars and to unveil the molecular bases of clonal phenotypic variation.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, Pablo. Instituto de Ciencias de la Vid y El Vino ; Consejo Superior de Investigaciones Cientificas;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; ArgentinaFil: Bree, Laura. No especifíca;Fil: Sola, Cristobal. No especifíca;Fil: Bergamin, Daniel. No especifíca;Fil: Tulle, Walter Daniel. 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: Gómez Talquenca, Sebastián. Instituto Nacional de Tecnología Agropecuaria; ArgentinaFil: Lanz, Christa. Max Planck Institute for Biology of Ageing; AlemaniaFil: Royo, Carolina. Universidad de La Rioja; EspañaFil: Ibañez, Javier. Universidad de La Rioja; EspañaFil: Martínez Zapater, José M.. Universidad de La Rioja; EspañaFil: Weigel, Detlef. Max Planck Institute for Biology of Ageing; AlemaniaFil: 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; ArgentinaOxford University Press2024-05info:eu-repo/semantics/articleinfo:eu-repo/semantics/publishedVersionhttp://purl.org/coar/resource_type/c_6501info:ar-repo/semantics/articuloapplication/pdfapplication/pdfapplication/pdfhttp://hdl.handle.net/11336/241295Calderón, Pablo Luciano Sebastian; Carbonell Bejerano, Pablo; Muñoz, Claudio Javier; Bree, Laura; Sola, Cristobal; et al.; Diploid genome assembly of the Malbec grapevine cultivar enables haplotype-aware analysis of transcriptomic differences underlying clonal phenotypic variation; Oxford University Press; Horticulture Research; 11; 5; 5-2024; 1-202052-7276CONICET DigitalCONICETenginfo:eu-repo/semantics/altIdentifier/doi/10.1093/hr/uhae080info:eu-repo/semantics/altIdentifier/url/https://academic.oup.com/hr/article/11/5/uhae080/7628331info:eu-repo/semantics/openAccesshttps://creativecommons.org/licenses/by-nc-sa/2.5/ar/reponame:CONICET Digital (CONICET)instname:Consejo Nacional de Investigaciones Científicas y Técnicas2025-09-29T09:57:24Zoai:ri.conicet.gov.ar:11336/241295instacron: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 09:57:24.396CONICET Digital (CONICET) - Consejo Nacional de Investigaciones Científicas y Técnicasfalse |
dc.title.none.fl_str_mv |
Diploid genome assembly of the Malbec grapevine cultivar enables haplotype-aware analysis of transcriptomic differences underlying clonal phenotypic variation |
title |
Diploid genome assembly of the Malbec grapevine cultivar enables haplotype-aware analysis of transcriptomic differences underlying clonal phenotypic variation |
spellingShingle |
Diploid genome assembly of the Malbec grapevine cultivar enables haplotype-aware analysis of transcriptomic differences underlying clonal phenotypic variation Calderón, Pablo Luciano Sebastian MALBEC GENOME GRAPEVINE VITIS RNA-SEQ |
title_short |
Diploid genome assembly of the Malbec grapevine cultivar enables haplotype-aware analysis of transcriptomic differences underlying clonal phenotypic variation |
title_full |
Diploid genome assembly of the Malbec grapevine cultivar enables haplotype-aware analysis of transcriptomic differences underlying clonal phenotypic variation |
title_fullStr |
Diploid genome assembly of the Malbec grapevine cultivar enables haplotype-aware analysis of transcriptomic differences underlying clonal phenotypic variation |
title_full_unstemmed |
Diploid genome assembly of the Malbec grapevine cultivar enables haplotype-aware analysis of transcriptomic differences underlying clonal phenotypic variation |
title_sort |
Diploid genome assembly of the Malbec grapevine cultivar enables haplotype-aware analysis of transcriptomic differences underlying clonal phenotypic variation |
dc.creator.none.fl_str_mv |
Calderón, Pablo Luciano Sebastian Carbonell Bejerano, Pablo Muñoz, Claudio Javier Bree, Laura Sola, Cristobal Bergamin, Daniel Tulle, Walter Daniel Gómez Talquenca, Sebastián Lanz, Christa Royo, Carolina Ibañez, Javier Martínez Zapater, José M. Weigel, Detlef Lijavetzky, Diego Claudio |
author |
Calderón, Pablo Luciano Sebastian |
author_facet |
Calderón, Pablo Luciano Sebastian Carbonell Bejerano, Pablo Muñoz, Claudio Javier Bree, Laura Sola, Cristobal Bergamin, Daniel Tulle, Walter Daniel Gómez Talquenca, Sebastián Lanz, Christa Royo, Carolina Ibañez, Javier Martínez Zapater, José M. Weigel, Detlef Lijavetzky, Diego Claudio |
author_role |
author |
author2 |
Carbonell Bejerano, Pablo Muñoz, Claudio Javier Bree, Laura Sola, Cristobal Bergamin, Daniel Tulle, Walter Daniel Gómez Talquenca, Sebastián Lanz, Christa Royo, Carolina Ibañez, Javier Martínez Zapater, José M. Weigel, Detlef Lijavetzky, Diego Claudio |
author2_role |
author author author author author author author author author author author author author |
dc.subject.none.fl_str_mv |
MALBEC GENOME GRAPEVINE VITIS RNA-SEQ |
topic |
MALBEC GENOME GRAPEVINE VITIS RNA-SEQ |
purl_subject.fl_str_mv |
https://purl.org/becyt/ford/1.6 https://purl.org/becyt/ford/1 |
dc.description.none.fl_txt_mv |
To preserve their varietal attributes established grapevine cultivars (Vitis vinifera L. ssp. vinifera) must be clonally propagated, due to their highly heterozygous genomes. Malbec is a France-originated cultivar appreciated for producing high-quality wines, and is the offspring of cultivars Prunelard and Magdeleine Noire des Charentes. Here, we have built a diploid genome assembly of Malbec, after trio binning of PacBio long reads into the two haploid complements inherited from either parent. After haplotype-aware deduplication and corrections, complete assemblies for the two haplophases were obtained with very low haplotype switch-error rate (<0.025). The haplophases alignment identified >25% of polymorphic regions. Gene annotation including RNA-seq transcriptome assembly and ab initio prediction evidence resulted in similar gene model numbers for both haplophases. The annotated diploid assembly was exploited in the transcriptomic comparison of four clonal accessions of Malbec that exhibited variation in berry composition traits. Analysis of the ripening pericarp transcriptome using either haplophases as reference yielded similar results, although some differences were observed. Particularly, among the differentially expressed genes identified only with the Magdeleine-inherited haplotype as reference, we observed an over-representation of hypothetically hemizygous genes. The higher berry anthocyanin content of clonal accession 595 was associated with increased abscisic acid responses, possibly leading to the observed overexpression of phenylpropanoid metabolism genes and deregulation of genes associated to abiotic stress response. Overall, the results highlight the importance of producing diploid assemblies to fully represent the genomic diversity of highly heterozygous woody crop cultivars and to unveil the molecular bases of clonal phenotypic variation. 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, Pablo. Instituto de Ciencias de la Vid y El Vino ; Consejo Superior de Investigaciones Cientificas; 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, Cristobal. No especifíca; Fil: Bergamin, Daniel. No especifíca; Fil: Tulle, Walter Daniel. 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: Gómez Talquenca, Sebastián. Instituto Nacional de Tecnología Agropecuaria; Argentina Fil: Lanz, Christa. Max Planck Institute for Biology of Ageing; Alemania Fil: Royo, Carolina. Universidad de La Rioja; España Fil: Ibañez, Javier. Universidad de La Rioja; España Fil: Martínez Zapater, José M.. Universidad de La Rioja; España Fil: Weigel, Detlef. Max Planck Institute for Biology of Ageing; Alemania 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 |
description |
To preserve their varietal attributes established grapevine cultivars (Vitis vinifera L. ssp. vinifera) must be clonally propagated, due to their highly heterozygous genomes. Malbec is a France-originated cultivar appreciated for producing high-quality wines, and is the offspring of cultivars Prunelard and Magdeleine Noire des Charentes. Here, we have built a diploid genome assembly of Malbec, after trio binning of PacBio long reads into the two haploid complements inherited from either parent. After haplotype-aware deduplication and corrections, complete assemblies for the two haplophases were obtained with very low haplotype switch-error rate (<0.025). The haplophases alignment identified >25% of polymorphic regions. Gene annotation including RNA-seq transcriptome assembly and ab initio prediction evidence resulted in similar gene model numbers for both haplophases. The annotated diploid assembly was exploited in the transcriptomic comparison of four clonal accessions of Malbec that exhibited variation in berry composition traits. Analysis of the ripening pericarp transcriptome using either haplophases as reference yielded similar results, although some differences were observed. Particularly, among the differentially expressed genes identified only with the Magdeleine-inherited haplotype as reference, we observed an over-representation of hypothetically hemizygous genes. The higher berry anthocyanin content of clonal accession 595 was associated with increased abscisic acid responses, possibly leading to the observed overexpression of phenylpropanoid metabolism genes and deregulation of genes associated to abiotic stress response. Overall, the results highlight the importance of producing diploid assemblies to fully represent the genomic diversity of highly heterozygous woody crop cultivars and to unveil the molecular bases of clonal phenotypic variation. |
publishDate |
2024 |
dc.date.none.fl_str_mv |
2024-05 |
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 |
http://hdl.handle.net/11336/241295 Calderón, Pablo Luciano Sebastian; Carbonell Bejerano, Pablo; Muñoz, Claudio Javier; Bree, Laura; Sola, Cristobal; et al.; Diploid genome assembly of the Malbec grapevine cultivar enables haplotype-aware analysis of transcriptomic differences underlying clonal phenotypic variation; Oxford University Press; Horticulture Research; 11; 5; 5-2024; 1-20 2052-7276 CONICET Digital CONICET |
url |
http://hdl.handle.net/11336/241295 |
identifier_str_mv |
Calderón, Pablo Luciano Sebastian; Carbonell Bejerano, Pablo; Muñoz, Claudio Javier; Bree, Laura; Sola, Cristobal; et al.; Diploid genome assembly of the Malbec grapevine cultivar enables haplotype-aware analysis of transcriptomic differences underlying clonal phenotypic variation; Oxford University Press; Horticulture Research; 11; 5; 5-2024; 1-20 2052-7276 CONICET Digital CONICET |
dc.language.none.fl_str_mv |
eng |
language |
eng |
dc.relation.none.fl_str_mv |
info:eu-repo/semantics/altIdentifier/doi/10.1093/hr/uhae080 info:eu-repo/semantics/altIdentifier/url/https://academic.oup.com/hr/article/11/5/uhae080/7628331 |
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 |
dc.publisher.none.fl_str_mv |
Oxford University Press |
publisher.none.fl_str_mv |
Oxford University Press |
dc.source.none.fl_str_mv |
reponame:CONICET Digital (CONICET) instname:Consejo Nacional de Investigaciones Científicas y Técnicas |
reponame_str |
CONICET Digital (CONICET) |
collection |
CONICET Digital (CONICET) |
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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1844613717651619840 |
score |
13.070432 |