High quality genome assembly of the brown hare (Lepus europaeus) with chromosome-level scaffolding

Abstract

Here we present a high-quality genome assembly of the mountain hare (Lepus timidusL.), based on a fibroblast cell line of a male specimen from Ilomantsi, Eastern Finland. The mountain hare represents the first Finnish contribution 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 utilizing a Hi-C chromosome structure capture approach. After manual curation, the assembled genome length was 2,930,972,003 bp with N50 125.8Mb. 93.16% of the assembly could be assigned to 25 identified chromosomes (23 autosomes plus X and Y), matching the published karyotype. The chromosomes were named 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.Compared to the previous pseudoreference genome ofL. timidusssp.hibernicusBell, assembled using the rabbit genome, this new reference genome represents the nominal subspecies and the species-specific chromosomal conformation. In addition to providing a useful comparison for population studies, the genome can offer insight into the chromosomal evolution among Glires in general and Lagomorpha in particular. The chromosomal assembly of the genome also demonstrates that the cell line has not gone through karyotypic changes during culture.