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

Author:

Nebenführ Marcel123ORCID,Prochotta David123ORCID,Ben Hamadou Alexander13ORCID,Janke Axel123ORCID,Gerheim Charlotte13ORCID,Betz Christian4,Greve Carola13ORCID,Bolz Hanno Jörn4ORCID

Affiliation:

1. Senckenberg Biodiversity and Climate Research Centre (BiK-F), Frankfurt am Main, Germany

2. Institute for Ecology, Evolution, and Diversity, Goethe University, Frankfurt am Main, Germany

3. LOEWE-Centre for Translational Biodiversity Genomics (TBG), Frankfurt am Main, Germany

4. Bioscientia Human Genetics, Institute for Medical Diagnostics GmbH, Ingelheim, Germany

Abstract

The time required for genome sequencing and de novo assembly depends on the interaction between laboratory work, sequencing capacity, and the bioinformatics workflow, often constrained by external sequencing services. Bringing together academic biodiversity institutes and a medical diagnostics company with extensive sequencing capabilities, we aimed at generating a high-quality mammalian de novo genome in minimal time. We present the first chromosome-level genome assembly of the Whippet, using PacBio long-read high-fidelity sequencing and reference-guided scaffolding. 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. Annotation using mammalian genomes and transcriptome data yielded 28,383 transcripts, 90.9% complete BUSCO genes, and identified 36.5% repeat content. Sequencing, assembling, and scaffolding the chromosome-level genome of the Whippet took less than a week, adding another high-quality reference genome to the available sequences of domestic dog breeds.

Funder

Hessen State Ministry of Higher Education, Research and the Arts

Publisher

GigaScience Press

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