A chromosome-level genome assembly for snowshoe hare (Lepus americanus).

Abstract

The snowshoe hare (Lepus americanus) is considered a critical keystone species of the boreal and temperate forests of North America. Although their population ecology and evolutionary dynamics have been studied extensively, a lack of high-quality genomic resources has limited molecular insights into their biology. Here, we combined cytogenetic karyotype analysis, PacBio HiFi long-read sequencing (~33× coverage), and chromosome conformation capture (Hi-C) sequencing to generate a phased chromosome-level genome assembly from a male snowshoe hare specimen. The primary haploid assembly is 2.75 Gb, with the 24 largest scaffolds corresponding to individual chromosomes (2n = 48 chromosomes, scaffold N50 = 131 Mb) and containing only 213 gaps. Assembly completeness was high, with 99.6% of mammalian Benchmarking Universal Single-Copy Orthologs recovered. Comparative analysis of this genome with other Lepus species revealed conservation of chromosomal architecture within the genus, while alignment with the European rabbit (Oryctolagus cuniculus) genome identified chromosomal rearrangements consistent with known karyotypic divergence between hares and rabbits. This genome assembly establishes a critical reference for future genomic studies in snowshoe hares and related taxa.