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Abstract
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’ [ver mas...]
dc.contributor.authorCalderon, Luciano
dc.contributor.authorCarbonell-Bejerano, Pablo
dc.contributor.authorMauri, Nuria
dc.contributor.authorMuñoz, Claudio
dc.contributor.authorBree, Laura
dc.contributor.authorSola, Cristóbal
dc.contributor.authorBergamin, Daniel
dc.contributor.authorGomez Talquenca, Gonzalo
dc.contributor.authorIbañez, Javier
dc.contributor.authorMartinez Zapater, José Miguel
dc.contributor.authorWeigel, D.
dc.contributor.authorLijavetzky, Diego
dc.date.accessioned2022-01-07T11:36:45Z
dc.date.available2022-01-07T11:36:45Z
dc.date.issued2022-01-07
dc.identifier.issn1852-6322
dc.identifier.urihttp://hdl.handle.net/20.500.12123/11075
dc.descriptionPoster. Publicado en: BAG Journal of Basic and Applied Genetics, 32 (1 suppl), 2021
dc.description.abstractMost 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. Postassembly, 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.eng
dc.formatapplication/pdfes_AR
dc.language.isoenges_AR
dc.publisherAsociación Latinoamericana de Genetica (ALAG)es_AR
dc.rightsinfo:eu-repo/semantics/openAccesses_AR
dc.sourceXVIII 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, V Congreso Latinoamericano de Genética Humana. Valdivia, Chile, 5-8 octubre 2021 (modalidad virtual)es_AR
dc.subjectVides_AR
dc.subjectGrapevineseng
dc.subjectHaplotiposes_AR
dc.subjectHaplotypeseng
dc.subjectHeterocigotoses_AR
dc.subjectHeterozygoteseng
dc.subjectGenomases_AR
dc.subjectGenomeseng
dc.subjectDiploidiaes_AR
dc.subjectDiploidyeng
dc.subjectFitomejoramientoes_AR
dc.subjectPlant Breedingeng
dc.subject.otherMalbeces_AR
dc.titleDe novo assembly of separate haplotypes solves the high-heterozygosity inconvenience of grapevine genomeses_AR
dc.title.alternativeA completely-phased diploid genome assembly for ‘Malbec’ cultivar (Vitis vinifera L.)es_AR
dc.typeinfo:ar-repo/semantics/documento de conferenciaes_AR
dc.typeinfo:eu-repo/semantics/conferenceObjectes_AR
dc.typeinfo:eu-repo/semantics/publishedVersiones_AR
dc.description.origenEEA Mendozaes_AR
dc.description.filFil: Calderón, Luciano. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Mendoza. Instituto de Biología Agrícola de Mendoza; Argentina. Universidad Nacional de Cuyo. Facultad de Ciencias Agrarias. Instituto de Biología Agrícola de Mendoza; Argentinaes_AR
dc.description.filFil: Carbonell-Bejerano, P. Max Planck Institute for Developmental Biology; Alemaniaes_AR
dc.description.filFil: Mauri, Nuria. Instituto de Ciencias de la Vid y del Vino (CSIC, UR, Gobierno de La Rioja). Finca La Grajera; Argentinaes_AR
dc.description.filFil: Muñoz, C. Universidad Nacional de Cuyo. Facultad de Ciencias Agrarias; Argentinaes_AR
dc.description.filFil: Bree, Laura. Vivero Mercier; Argentinaes_AR
dc.description.filFil: Sola, Cristóbal. Vivero Mercier; Argentinaes_AR
dc.description.filFil: Bergamin, Daniel. Vivero Mercier; Argentinaes_AR
dc.description.filFil: Gomez Talquenca, Gonzalo. Instituto Nacional de Tecnología Agropecuaria (INTA). Estación Experimental Agropecuaria Mendoza; Argentinaes_AR
dc.description.filFil: Martínez Zapater, José Miguel. Instituto de Ciencias de la Vid y del Vino (CSIC, UR, Gobierno de La Rioja). Finca La Grajera; Argentinaes_AR
dc.description.filFil: Weigel, D. Max Planck Institute for Developmental Biology; Alemaniaes_AR
dc.description.filFil: Lijavetzky, Diego. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Mendoza. Instituto de Biología Agrícola de Mendoza; Argentina. Universidad Nacional de Cuyo. Facultad de Ciencias Agrarias. Instituto de Biología Agrícola de Mendoza; Argentinaes_AR
dc.subtypeponencia


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