Whole-genome sequencing of 2 bovins trio

Following the Genome in a Bottle project example, we sequenced one Charolais heifer with eight different technologies: Illumina paired-end, Oxford Nanopore (R9.4.1 and Q20+), Pacific Biosciences (HiFi and CLR), 10X Genomics linked-reads, and Hi-C reads. In order to generate haplotypic assemblies, we also sequenced both parents with short (Illumina) and long (ONT) reads. From this data webuilt six high quality reference genomes using up-to-date software packages in order to assessread quality. The PacBio HiFi assembly shows better metrics than reference ARS-UCD1.2: total length of 3.2 GB and contig N50 of 87.6 Mb. BUSCO assessment finds 95.8% of complete highly conserved mammal genes in this assembly. We also identified 36,313 structural variants larger than 50 base pairs. This assembly is a contribution to the bovine pangenome for the “Charolais” breed. The read sets are building blocks enabling the community to gain novel insight on sequencing technologies for applications such as SNP, indel or structural variant calling,and de novo assembly. This project is a part of SeqOccIn project.