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

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 and 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 Vertebrate Genomes Project 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, the mat consists of only 166 contigs with an N50 of 39 Mbp. BUSCO (Benchmarking Universal Single-Copy Orthologue) analysis showed 95.4% completeness based on Carnivora conservative genes (carnivora_odb10). When compared with other available genomes from subtribe Canina, the quality of the assembly is excellent, typically between the first and third 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.