De novo assembly of 90 bovines genomes using PacBio CLR application comparison and optimization
Résumé
GeT-PlaGe is a genomic core facility which provides access to technologies and expertise in genome sequencing to academic and private research teams. The SeqOccIn (Sequencing Occitanie Innovation) project, managed by Get-PlaGe and Genotoul Bioinfo platforms, was selected by the Occitanie Region as part of the call for projects "Regional Research and Innovation Platforms". The main objective is to acquire expertise on the optimal combination of long fragment sequencing technologies and associated applications to better characterize complex genomes in the agronomical field: from SNP and structural variation detection, to high quality assembly production. These approaches have allowed to assemble a novel high quality bovine reference genome. We chose to identify single nucleotide polymorphisms and structural variants (insertions and deletions) by comparing multiple assemblies. A preliminary study done on a heifer (37160) showed that long-reads sequencing is the most suitable solution for structural variations detection. We sequenced 154 bulls from 14 breeds with PacBio Sequel II Continuous Long-Read (CLR). Here we present assembly as well as variation detection results for 90 bulls from 11 breeds (9 Abondances, 7 Aubracs, 4 Blondes d’Aquitaine, 3 Charolaises, 14 Holsteins, 11 Limousines, 19 Montbeliardes, 14 Normandes, 3 Rouges Flamandes, 2 Tarentaises and 4 Vosgiennes)
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