Chromosome-level genome of the European hamster (Cricetus cricetus) and its genome-wide population structure across Western Europe

Abstract Background The European hamster (Cricetus cricetus) was once a pest on European farmland, but its numbers have declined dramatically in recent decades, making it a critically endangered species throughout Europe and beyond. While it is strictly protected by EU law and several conservations, breeding and release programs have been initiated, and little is known about the level of genetic erosion and inbreeding on a European scale. Results Here, we present a chromosome-level de novo genome of a female hamster and a first population genomic analysis from the western range of the species’ distribution, using Illumina short reads (10 × coverage) from 34 individuals. The genome is 2.89 Gbp long, with 11 chromosome-level scaffolds and around 600 unplaced scaffolds and scaffolds N50 of 267 Mbp. The genome is above the average length of a mammalian genome and longer than that of other studied hamster species. Four distinct hamster populations with no admixture can be identified, indicating highly isolated populations with limited connectivity. Heterozygosity (Ho) is generally low (< 0.05%, comparable to polar bears) with some exceptions of populations with Ho near zero and a few with Ho as high as 0.2%. Conclusions Most dramatically, the genomes of individuals used as founders for conservation breeding programs show exceptionally long runs of homozygosity, questioning its long-term suitability. This study confirms earlier concerns about the dramatically decreasing genetic diversity of the European hamster and provides a basis for future conservation efforts, which require consideration of population genetic factors.