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Major contribution to the bovine pangenome: whole genome sequences, SNPs, and structural variants of 154 bulls from 14 breeds
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International audience. Currently, most bovine studies are based on the Dominette ARS-UCD1.2 cow, but newly discovered sequences are missing from this Hereford assembly. Anomaly detection chips are incomplete, and structural variation analysis using short reads remains difficult. This is the background against which the Sequencing Occitanie Innovation (SeqOccIn) project was born. The main objective is to acquire expertise on the optimal combination of long fragment sequencing technologies and related applications to better characterise complex genomes in the agronomic field. In our first publication, we contributed to the bovine pangenome by producing a high-quality haplotype assembly for the Charolais breed. We chose to investigate single nucleotide polymorphisms and structural variants (insertions and deletions) by comparing several assemblies. This recent study has shown that long-read sequencing is the most suitable solution for detecting structural variations. Using PacBio Sequel II Continuous Long-Read (CLR) and Illumina 15X, we sequenced 154 bulls from 14 breeds (Holstein, Montbéliarde, Normande, Brune, Simmental, Abondance, Tarentaise, Vosgienne, Blonde d'Aquitaine, Charolaise, Limousine, Aubrac, Flamande, Parthenaise). These datasets will provide a useful resource for the community to better understand sequencing technologies for applications such as the identification of SNPs, indels or structural variants, and de novo assembly.
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