A COMPLETELY PHASED DIPLOID GENOME ASSEMBLY FOR MALBEC CULTIVAR (Vitis vinifera L.)

CALDERÓN LUCIANO; CARBONELL-BEJERANO, PABLO; MUÑOZ, CLAUDIO; LIJAVETZKY, DIEGO

Valdivia

Congreso; ALAG 2021; 2021

Asociación Latinoamericana de Genética

Most grapevine cultivars originated from outcrossing two genetically diverse parents, andare 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 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.