Work

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

Year: 2024

Type: article

Abstract: 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.

Source: Gigabyte

DOI: 10.46471/gigabyte.134