A chromosome phased diploid genome assembly of African hunting dog (Lycaon pictus).

Abstract

The African hunting dog (Lycaon pictus, 2n=78) once ranged over most sub-Saharan ecosystems except its deserts and rainforests. However as a result of (still ongoing) population declines, today they remain only as small fragmented populations. Furthermore, the future of the species remains unclear, due to both anthropogenic pressure as well as interactions with domestic dogs, thus their preservation is a conservation priority. On the tree of life, the hunting dog is basal to Canis and Cuon and forms a crown group with them, making it a useful species for comparative genomic studies. Here, we present a diploid chromosome level assembly of an African hunting dog. Assembled according to VGP guidelines from a combination of PacBio HiFi reads and HiC data, it is phased at the level of individual chromosomes. The maternal (pseudo)haplotype (mat) of our assembly has a length of 2.38 Gbp, and 99.36 % of the sequence is encompassed by 39 chromosomal scaffolds. The rest is included in only 36 unplaced short scaffolds. At the contig level, mat consists of only 166 contigs with an N50 of 39 Mbp. BUSCO analysis showed 95.4 % completeness based on Сarnivora conservative genes (carnivora_odb10). When compared to other available genomes from subtribe Canina, the quality of the assembly is excellent, typically between the 1st and 3rd depending on the parameter used, and a significant improvement on previously published genomes for the species. We hope this assembly will play an important role in future conservation efforts and comparative studies of canid genomes.