A high quality reference genome of the brown hare

Abstract

We present here a high-quality genome assembly of the brown hare (Lepus europaeus Pallas), based on a fibroblast cell line of a male specimen from Liperi, Eastern Finland. This brown hare genome represents the first Finnish contribuSon to the European Reference Genome Atlas pilot effort to generate reference genomes for European biodiversity.The genome was assembled using 25X PacBio HiFi sequencing data and scaffolded uSlizing a Hi-C chromosome structure capture approach. A]er manual curaSon, the assembled genome length was 2,930,972,003 bp with N50 scaffold of 125.8 Mb. 93.16% of the assembly could be assigned to 25 idenSfied chromosomes (23 autosomes plus X and Y), matching the published karyotype. The chromosomes were numbered according to size. The genome has a high degree of completeness based on the BUSCO score (mammalia_odb10 database), Complete: 96.1% [Single copy: 93.1%, Duplicated: 3.0%], Fragmented 0.8%, and Missing 2.9%. The mitochondrial genome of the cell line was sequenced and assembled separately.The brown hare genome is parScularly interesSng as this species readily hybridizes with the mountain hare (Lepus *midus L.) at the species contact zone in northern Eurasia,ferSle offspring and resulSng in gene flow between the two species. In addiSon to providing a useful comparison for populaSon studies, the genome can offer insight into the chromosomal evoluSon among Glires in general and Lagomorpha in parScular. The chromosomal assembly of the genome also demonstrates that the cell line has not acquired karyotypic changes during culture.