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

The Siberian flying squirrel (<i>Pteromys volans</i>) 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 <i>Least Concern</i> throughout their immense Eurasian distribution, this species is red-listed as <i>Vulnerable</i> and even <i>Critically Endangered</i> 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 <i>P. volans</i> (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 <i>k</i>-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, <i>P. volans</i> 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 (<i>Pteromys volans volans</i>). While overall considered to be of <i>Least Concern</i> 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.