De novo assembly of separate haplotypes solves the high-heterozygosity inconvenience of grapevine genomes

• Autores: Calderon, Luciano; Carbonell-Bejerano, Pablo; Mauri, Nuria; Muñoz, Claudio; Bree, Laura; Sola, Cristóbal; Bergamin, Daniel; Gomez Talquenca, Gonzalo; Ibañez, Javier; Martinez Zapater, José Miguel; Weigel, D.; Lijavetzky, Diego
• Año de publicación: 2022
• Idioma: inglés
• Tipo de recurso: documento de conferencia
• Fuente: 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, V Congreso Latinoamericano de Genética Humana. Valdivia, Chile, 5-8 octubre 2021 (modalidad virtual)
• Materia: Vid; Haplotipos; Heterocigotos; Genomas; Diploidia; Fitomejoramiento; Grapevines; Haplotypes; Heterozygotes; Genomes; Diploidy; Plant Breeding; Malbec
• Institución: Instituto Nacional de Tecnología Agropecuaria

Poster. Publicado en: BAG Journal of Basic and Applied Genetics, 32 (1 suppl), 2021
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. 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.
EEA Mendoza
Fil: 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; Argentina
Fil: Carbonell-Bejerano, P. Max Planck Institute for Developmental Biology; Alemania
Fil: Mauri, Nuria. Instituto de Ciencias de la Vid y del Vino (CSIC, UR, Gobierno de La Rioja). Finca La Grajera; España
Fil: Muñoz, C. Universidad Nacional de Cuyo. Facultad de Ciencias Agrarias; Argentina
Fil: Bree, Laura. Vivero Mercier; Argentina
Fil: Sola, Cristóbal. Vivero Mercier; Argentina
Fil: Bergamin, Daniel. Vivero Mercier; Argentina
Fil: Gomez Talquenca, Gonzalo. Instituto Nacional de Tecnología Agropecuaria (INTA). Estación Experimental Agropecuaria Mendoza; Argentina
Fil: Martínez Zapater, José Miguel. Instituto de Ciencias de la Vid y del Vino (CSIC, UR, Gobierno de La Rioja). Finca La Grajera; España
Fil: Weigel, D. Max Planck Institute for Developmental Biology; Alemania
Fil: 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; Argentina