High-speed whole-genome sequencing of a Whippet: Rapid chromosome-level assembly and annotation of an extremely fast dog’s genome

Background The time required for sequencing and de novo assembly of genomes is highly dependent on the interaction between laboratory work, sequencing capacity, and the bioinformatics workflow. As a result, genome projects are often not only limited by financial, computational and sequencing platform resources, but also delayed by second party sequencing service providers. By bringing together academic biodiversity institutes and a medical diagnostics company with extensive sequencing capabilities and know-how, we aimed at generating a high-quality mammalian de novo genome in the shortest possible time period. Therefore, we streamlined all processes involved and chose a very fast dog as a model: The Whippet.

Findings We present the first chromosome-level genome assembly of the Whippet. We used PacBio long-read HiFi sequencing and reference-guided scaffolding to generate a high-quality genome assembly. The final assembly has a contig N50 of 55 Mbp and a scaffold N50 of 65.7 Mbp. The total assembly length is 2.47 Gbp, of which 2.43 Gpb were scaffolded into 39 chromosome-length scaffolds. In addition, we used available mammalian genomes and transcriptome data to annotate the genome assembly. The annotation resulted in 28,383 transcripts resembling a total of 90.9% complete BUSCO genes and identified a repeat content of 36.5%.

Conclusions Sequencing, assembling, and scaffolding the chromosome-level genome of the Whippet took less than a week and adds a high-quality reference genome to the list of domestic dog breeds sequenced to date.