‘Nebbiolo’ genome assembly allows surveying the occurrence and functional implications of genomic structural variations in grapevines (Vitis vinifera L.)

Autores
Maestri, Simone; Gambino, Giorgio; Lopatriello, Giulia; Minio, Andrea; Perrone, Irene; Cosentino, Emanuela; Giovannone, Barbara; Marcolungo, Luca; Alfano, Massimiliano; Rombauts, Stephane; Cantu, Dario; Rossato, Marzia; Delledonne, Massimo; Calderón, Pablo Luciano Sebastian
Año de publicación
2022
Idioma
inglés
Tipo de recurso
artículo
Estado
versión publicada
Descripción
Background: ‘Nebbiolo’ is a grapevine cultivar typical of north-western Italy, appreciated for producing high-quality red wines. Grapevine cultivars are characterized by possessing highly heterozygous genomes, including a great incidence of genomic rearrangements larger than 50 bp, so called structural variations (SVs). Even though abundant, SVs are an under-explored source of genetic variation mainly due to methodological limitations at their detection. Results: We employed a multiple platform approach to produce long-range genomic data for two different ‘Nebbiolo’ clones, namely: optical mapping, long-reads and linked-reads. We performed a haplotype-resolved de novo assembly for cultivar ‘Nebbiolo’ (clone CVT 71) and used an ab-initio strategy to annotate it. The annotated assembly enhanced our ability to detect SVs, enabling the study of genomic regions not present in the grapevines’ reference genome and accounting for their functional implications. We performed variant calling analyses at three different organizational levels: i) between haplotypes of clone CVT 71 (primary assembly vs haplotigs), ii) between ‘Nebbiolo’ and ‘Cabernet Sauvignon’ assemblies and iii) between clones CVT 71 and CVT 185, representing different ‘Nebbiolo’ biotypes. The cumulative size of non-redundant merged SVs indicated a total of 79.6 Mbp for the first comparison and 136.1 Mbp for the second one, while no SVs were detected for the third comparison. Interestingly, SVs differentiating cultivars and haplotypes affected similar numbers of coding genes. Conclusions: Our results suggest that SVs accumulation rate and their functional implications in ‘Nebbiolo’ genome are highly-dependent on the organizational level under study. SVs are abundant when comparing ‘Nebbiolo’ to a different cultivar or the two haplotypes of the same individual, while they turned absent between the two analysed clones.
Fil: Maestri, Simone. Universita di Verona; Italia
Fil: Gambino, Giorgio. Centre National de la Recherche Scientifique; Francia
Fil: Lopatriello, Giulia. Universita di Verona; Italia
Fil: Minio, Andrea. University of California at Davis; Estados Unidos
Fil: Perrone, Irene. Centre National de la Recherche Scientifique; Francia
Fil: Cosentino, Emanuela. Universita di Verona; Italia
Fil: Giovannone, Barbara. Universita di Verona; Italia
Fil: Marcolungo, Luca. Universita di Verona; Italia
Fil: Alfano, Massimiliano. Universita di Verona; Italia
Fil: Rombauts, Stephane. University of Ghent; Bélgica
Fil: Cantu, Dario. University of California at Davis; Estados Unidos
Fil: Rossato, Marzia. Universita di Verona; Italia
Fil: Delledonne, Massimo. Universita di Verona; Italia
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
Materia
GENOMICS
STRUCTURAL VARIATIONS
NEBBIOLO
VITIS VINIFERA
Nivel de accesibilidad
acceso abierto
Condiciones de uso
https://creativecommons.org/licenses/by/2.5/ar/
Repositorio
CONICET Digital (CONICET)
Institución
Consejo Nacional de Investigaciones Científicas y Técnicas
OAI Identificador
oai:ri.conicet.gov.ar:11336/161431
Acceder
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oai_identifier_str oai:ri.conicet.gov.ar:11336/161431
network_acronym_str CONICETDig
repository_id_str 3498
network_name_str CONICET Digital (CONICET)
spelling ‘Nebbiolo’ genome assembly allows surveying the occurrence and functional implications of genomic structural variations in grapevines (Vitis vinifera L.)Maestri, SimoneGambino, GiorgioLopatriello, GiuliaMinio, AndreaPerrone, IreneCosentino, EmanuelaGiovannone, BarbaraMarcolungo, LucaAlfano, MassimilianoRombauts, StephaneCantu, DarioRossato, MarziaDelledonne, MassimoCalderón, Pablo Luciano SebastianGENOMICSSTRUCTURAL VARIATIONSNEBBIOLOVITIS VINIFERAhttps://purl.org/becyt/ford/1.6https://purl.org/becyt/ford/1https://purl.org/becyt/ford/1.2https://purl.org/becyt/ford/1https://purl.org/becyt/ford/4.1https://purl.org/becyt/ford/4Background: ‘Nebbiolo’ is a grapevine cultivar typical of north-western Italy, appreciated for producing high-quality red wines. Grapevine cultivars are characterized by possessing highly heterozygous genomes, including a great incidence of genomic rearrangements larger than 50 bp, so called structural variations (SVs). Even though abundant, SVs are an under-explored source of genetic variation mainly due to methodological limitations at their detection. Results: We employed a multiple platform approach to produce long-range genomic data for two different ‘Nebbiolo’ clones, namely: optical mapping, long-reads and linked-reads. We performed a haplotype-resolved de novo assembly for cultivar ‘Nebbiolo’ (clone CVT 71) and used an ab-initio strategy to annotate it. The annotated assembly enhanced our ability to detect SVs, enabling the study of genomic regions not present in the grapevines’ reference genome and accounting for their functional implications. We performed variant calling analyses at three different organizational levels: i) between haplotypes of clone CVT 71 (primary assembly vs haplotigs), ii) between ‘Nebbiolo’ and ‘Cabernet Sauvignon’ assemblies and iii) between clones CVT 71 and CVT 185, representing different ‘Nebbiolo’ biotypes. The cumulative size of non-redundant merged SVs indicated a total of 79.6 Mbp for the first comparison and 136.1 Mbp for the second one, while no SVs were detected for the third comparison. Interestingly, SVs differentiating cultivars and haplotypes affected similar numbers of coding genes. Conclusions: Our results suggest that SVs accumulation rate and their functional implications in ‘Nebbiolo’ genome are highly-dependent on the organizational level under study. SVs are abundant when comparing ‘Nebbiolo’ to a different cultivar or the two haplotypes of the same individual, while they turned absent between the two analysed clones.Fil: Maestri, Simone. Universita di Verona; ItaliaFil: Gambino, Giorgio. Centre National de la Recherche Scientifique; FranciaFil: Lopatriello, Giulia. Universita di Verona; ItaliaFil: Minio, Andrea. University of California at Davis; Estados UnidosFil: Perrone, Irene. Centre National de la Recherche Scientifique; FranciaFil: Cosentino, Emanuela. Universita di Verona; ItaliaFil: Giovannone, Barbara. Universita di Verona; ItaliaFil: Marcolungo, Luca. Universita di Verona; ItaliaFil: Alfano, Massimiliano. Universita di Verona; ItaliaFil: Rombauts, Stephane. University of Ghent; BélgicaFil: Cantu, Dario. University of California at Davis; Estados UnidosFil: Rossato, Marzia. Universita di Verona; ItaliaFil: Delledonne, Massimo. Universita di Verona; ItaliaFil: 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; ArgentinaBioMed Central2022-02info:eu-repo/semantics/articleinfo:eu-repo/semantics/publishedVersionhttp://purl.org/coar/resource_type/c_6501info:ar-repo/semantics/articuloapplication/pdfapplication/pdfhttp://hdl.handle.net/11336/161431Maestri, Simone; Gambino, Giorgio; Lopatriello, Giulia; Minio, Andrea; Perrone, Irene; et al.; ‘Nebbiolo’ genome assembly allows surveying the occurrence and functional implications of genomic structural variations in grapevines (Vitis vinifera L.); BioMed Central; BMC Genomics; 23; 1; 2-2022; 1-151471-2164CONICET DigitalCONICETenginfo:eu-repo/semantics/altIdentifier/url/https://bmcgenomics.biomedcentral.com/articles/10.1186/s12864-022-08389-9info:eu-repo/semantics/altIdentifier/doi/10.1186/s12864-022-08389-9info:eu-repo/semantics/openAccesshttps://creativecommons.org/licenses/by/2.5/ar/reponame:CONICET Digital (CONICET)instname:Consejo Nacional de Investigaciones Científicas y Técnicas2025-11-05T10:48:58Zoai:ri.conicet.gov.ar:11336/161431instacron: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:34982025-11-05 10:48:58.684CONICET Digital (CONICET) - Consejo Nacional de Investigaciones Científicas y Técnicasfalse
dc.title.none.fl_str_mv ‘Nebbiolo’ genome assembly allows surveying the occurrence and functional implications of genomic structural variations in grapevines (Vitis vinifera L.)
title ‘Nebbiolo’ genome assembly allows surveying the occurrence and functional implications of genomic structural variations in grapevines (Vitis vinifera L.)
spellingShingle ‘Nebbiolo’ genome assembly allows surveying the occurrence and functional implications of genomic structural variations in grapevines (Vitis vinifera L.)
Maestri, Simone
GENOMICS
STRUCTURAL VARIATIONS
NEBBIOLO
VITIS VINIFERA
title_short ‘Nebbiolo’ genome assembly allows surveying the occurrence and functional implications of genomic structural variations in grapevines (Vitis vinifera L.)
title_full ‘Nebbiolo’ genome assembly allows surveying the occurrence and functional implications of genomic structural variations in grapevines (Vitis vinifera L.)
title_fullStr ‘Nebbiolo’ genome assembly allows surveying the occurrence and functional implications of genomic structural variations in grapevines (Vitis vinifera L.)
title_full_unstemmed ‘Nebbiolo’ genome assembly allows surveying the occurrence and functional implications of genomic structural variations in grapevines (Vitis vinifera L.)
title_sort ‘Nebbiolo’ genome assembly allows surveying the occurrence and functional implications of genomic structural variations in grapevines (Vitis vinifera L.)
dc.creator.none.fl_str_mv Maestri, Simone
Gambino, Giorgio
Lopatriello, Giulia
Minio, Andrea
Perrone, Irene
Cosentino, Emanuela
Giovannone, Barbara
Marcolungo, Luca
Alfano, Massimiliano
Rombauts, Stephane
Cantu, Dario
Rossato, Marzia
Delledonne, Massimo
Calderón, Pablo Luciano Sebastian
author Maestri, Simone
author_facet Maestri, Simone
Gambino, Giorgio
Lopatriello, Giulia
Minio, Andrea
Perrone, Irene
Cosentino, Emanuela
Giovannone, Barbara
Marcolungo, Luca
Alfano, Massimiliano
Rombauts, Stephane
Cantu, Dario
Rossato, Marzia
Delledonne, Massimo
Calderón, Pablo Luciano Sebastian
author_role author
author2 Gambino, Giorgio
Lopatriello, Giulia
Minio, Andrea
Perrone, Irene
Cosentino, Emanuela
Giovannone, Barbara
Marcolungo, Luca
Alfano, Massimiliano
Rombauts, Stephane
Cantu, Dario
Rossato, Marzia
Delledonne, Massimo
Calderón, Pablo Luciano Sebastian
author2_role author
author
author
author
author
author
author
author
author
author
author
author
author
dc.subject.none.fl_str_mv GENOMICS
STRUCTURAL VARIATIONS
NEBBIOLO
VITIS VINIFERA
topic GENOMICS
STRUCTURAL VARIATIONS
NEBBIOLO
VITIS VINIFERA
purl_subject.fl_str_mv https://purl.org/becyt/ford/1.6
https://purl.org/becyt/ford/1
https://purl.org/becyt/ford/1.2
https://purl.org/becyt/ford/1
https://purl.org/becyt/ford/4.1
https://purl.org/becyt/ford/4
dc.description.none.fl_txt_mv Background: ‘Nebbiolo’ is a grapevine cultivar typical of north-western Italy, appreciated for producing high-quality red wines. Grapevine cultivars are characterized by possessing highly heterozygous genomes, including a great incidence of genomic rearrangements larger than 50 bp, so called structural variations (SVs). Even though abundant, SVs are an under-explored source of genetic variation mainly due to methodological limitations at their detection. Results: We employed a multiple platform approach to produce long-range genomic data for two different ‘Nebbiolo’ clones, namely: optical mapping, long-reads and linked-reads. We performed a haplotype-resolved de novo assembly for cultivar ‘Nebbiolo’ (clone CVT 71) and used an ab-initio strategy to annotate it. The annotated assembly enhanced our ability to detect SVs, enabling the study of genomic regions not present in the grapevines’ reference genome and accounting for their functional implications. We performed variant calling analyses at three different organizational levels: i) between haplotypes of clone CVT 71 (primary assembly vs haplotigs), ii) between ‘Nebbiolo’ and ‘Cabernet Sauvignon’ assemblies and iii) between clones CVT 71 and CVT 185, representing different ‘Nebbiolo’ biotypes. The cumulative size of non-redundant merged SVs indicated a total of 79.6 Mbp for the first comparison and 136.1 Mbp for the second one, while no SVs were detected for the third comparison. Interestingly, SVs differentiating cultivars and haplotypes affected similar numbers of coding genes. Conclusions: Our results suggest that SVs accumulation rate and their functional implications in ‘Nebbiolo’ genome are highly-dependent on the organizational level under study. SVs are abundant when comparing ‘Nebbiolo’ to a different cultivar or the two haplotypes of the same individual, while they turned absent between the two analysed clones.
Fil: Maestri, Simone. Universita di Verona; Italia
Fil: Gambino, Giorgio. Centre National de la Recherche Scientifique; Francia
Fil: Lopatriello, Giulia. Universita di Verona; Italia
Fil: Minio, Andrea. University of California at Davis; Estados Unidos
Fil: Perrone, Irene. Centre National de la Recherche Scientifique; Francia
Fil: Cosentino, Emanuela. Universita di Verona; Italia
Fil: Giovannone, Barbara. Universita di Verona; Italia
Fil: Marcolungo, Luca. Universita di Verona; Italia
Fil: Alfano, Massimiliano. Universita di Verona; Italia
Fil: Rombauts, Stephane. University of Ghent; Bélgica
Fil: Cantu, Dario. University of California at Davis; Estados Unidos
Fil: Rossato, Marzia. Universita di Verona; Italia
Fil: Delledonne, Massimo. Universita di Verona; Italia
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
description Background: ‘Nebbiolo’ is a grapevine cultivar typical of north-western Italy, appreciated for producing high-quality red wines. Grapevine cultivars are characterized by possessing highly heterozygous genomes, including a great incidence of genomic rearrangements larger than 50 bp, so called structural variations (SVs). Even though abundant, SVs are an under-explored source of genetic variation mainly due to methodological limitations at their detection. Results: We employed a multiple platform approach to produce long-range genomic data for two different ‘Nebbiolo’ clones, namely: optical mapping, long-reads and linked-reads. We performed a haplotype-resolved de novo assembly for cultivar ‘Nebbiolo’ (clone CVT 71) and used an ab-initio strategy to annotate it. The annotated assembly enhanced our ability to detect SVs, enabling the study of genomic regions not present in the grapevines’ reference genome and accounting for their functional implications. We performed variant calling analyses at three different organizational levels: i) between haplotypes of clone CVT 71 (primary assembly vs haplotigs), ii) between ‘Nebbiolo’ and ‘Cabernet Sauvignon’ assemblies and iii) between clones CVT 71 and CVT 185, representing different ‘Nebbiolo’ biotypes. The cumulative size of non-redundant merged SVs indicated a total of 79.6 Mbp for the first comparison and 136.1 Mbp for the second one, while no SVs were detected for the third comparison. Interestingly, SVs differentiating cultivars and haplotypes affected similar numbers of coding genes. Conclusions: Our results suggest that SVs accumulation rate and their functional implications in ‘Nebbiolo’ genome are highly-dependent on the organizational level under study. SVs are abundant when comparing ‘Nebbiolo’ to a different cultivar or the two haplotypes of the same individual, while they turned absent between the two analysed clones.
publishDate 2022
dc.date.none.fl_str_mv 2022-02
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/11336/161431
Maestri, Simone; Gambino, Giorgio; Lopatriello, Giulia; Minio, Andrea; Perrone, Irene; et al.; ‘Nebbiolo’ genome assembly allows surveying the occurrence and functional implications of genomic structural variations in grapevines (Vitis vinifera L.); BioMed Central; BMC Genomics; 23; 1; 2-2022; 1-15
1471-2164
CONICET Digital
CONICET
url http://hdl.handle.net/11336/161431
identifier_str_mv Maestri, Simone; Gambino, Giorgio; Lopatriello, Giulia; Minio, Andrea; Perrone, Irene; et al.; ‘Nebbiolo’ genome assembly allows surveying the occurrence and functional implications of genomic structural variations in grapevines (Vitis vinifera L.); BioMed Central; BMC Genomics; 23; 1; 2-2022; 1-15
1471-2164
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://bmcgenomics.biomedcentral.com/articles/10.1186/s12864-022-08389-9
info:eu-repo/semantics/altIdentifier/doi/10.1186/s12864-022-08389-9
dc.rights.none.fl_str_mv info:eu-repo/semantics/openAccess
https://creativecommons.org/licenses/by/2.5/ar/
eu_rights_str_mv openAccess
rights_invalid_str_mv https://creativecommons.org/licenses/by/2.5/ar/
dc.format.none.fl_str_mv application/pdf
application/pdf
dc.publisher.none.fl_str_mv BioMed Central
publisher.none.fl_str_mv BioMed Central
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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