Chromosome-Level Reference Genome of an Endemic, Endangered Long-Armed Scarab (Cheirotonus formosanus): Discovery of a Putative Y-Linked Scaffold and Demographic History.

We present a high-quality, chromosome-level reference genome for the endangered, endemic long-armed scarab beetle Cheirotonus formosanus from Taiwan. Using PacBio HiFi and Hi-C data, the nuclear assembly spans 600.9 Mb with N 50 of 69.5 Mb (largest scaffold 93.2 Mb). BUSCO completeness is 99.3% for the assembly and 97.7% for the genome annotation. The circularized mitochondrial genome (20,286 bp: GC content 30.74%) contains the canonical 37 genes, and HiFi long reads resolve tandem repeats in the control region that are intractable with short read platforms. A chromosome-quotient approach with male (PacBio HiFi) and female (Illumina) reads assigned nine autosomal scaffolds, one X-linked, and a putative Y-linked scaffold (1.1 Mb). Historical demographic inferred independently from male and female genomes reveal identical trajectories. These results show a moderate effective population size (N e ) through most of the last ~500 thousand years ago (kya) and increase beginning ~115 kya with a peak around ~50 kya, followed by a decline toward the Last Glacial Period and relative stability in the Holocene. Recent demographic inference and analysis of runs of homozygosity (ROH) indicate that while N e has remained low, the genomic landscape is dominated by short homozygous segments (< 1 Mbp). The absence of very long ROH (> 5 Mbp) suggests that current inbreeding levels result from long-term historical restriction rather than recent consanguineous mating. Together, these resources and workflows enable sex-chromosome characterization, comparative mitochondrial genomics, and cross-timescale demographic inference in C. formosanus and provide reusable pipelines for beetle genomics and conservation.