A Prelude to Conservation Genomics: First Chromosome‐Level Genome Assembly of a Flying Squirrel (Pteromyini: Pteromys volans )

The Siberian flying squirrel ( Pteromys volans ) represents the only European Pteromyini species. Thus, it is biogeographically unique due to its specialised anatomy and biology as a volant rodent. As a result of habitat fragmentation and destruction, Siberian flying squirrels experience severe and ongoing population declines throughout most of their distribution. While considered Least Concern throughout their immense Eurasian distribution, this species is red‐listed as Vulnerable and even Critically Endangered in parts of its range. More knowledge about the population structure and overall biology is needed to improve conservation efforts for this umbrella and flagship species of old‐growth boreal forests. Here, we present the first chromosome‐level genome assembly of any Pteromyini, represented by P. volans (Uoulu_pteVol_1.0). The final assembly has a total length of 2.85 Gbp in 19 chromosome‐scale scaffolds with only minor differences in the chromosomal structure compared to other Sciuridae. All chromosome‐scale scaffolds show indications for telomeres at both ends; the N50 value and busco as well as k ‐mer completeness scores are high with 157.39 Mbp and 97%–99%, respectively, indicating chromosome‐level quality of the assembly. Based on whole‐genome data from 17 rodent species, P. volans clusters according to known evolutionary relationships. Additionally, we present a new 16,511 bp long mitogenome unveiling differences from known conspecific mitogenomes. We propose the utility of the new reference genome for further research and development of conservation‐applied genetic methods. Here, we present the first chromosome‐level genome assembly of any flying squirrel species (Pteromyini), specifically from the nominate subspecies of the Siberian flying squirrel ( Pteromys volans volans ). While overall considered to be of Least Concern by the IUCN, this species shows drastically declining trends in most of their distribution and is even threatened by extinction in some countries. Many studies pointed out that a genomic approach is needed to tackle current study questions comprehensively. Therefore, the novel chromosome‐level genome assembly should serve as a reference for research of the species' ecology and evolution as well as for the development of genetic tools for conservation management.