Capreolus pygargus Genome sequencing and assembly

The ancient mitochondrial genome of a Siberian roe deer (Capreolus pygargus) coded as XTS03G from Xiaotangshan Site was obtained by high throughput sequencing. The damage pattern demonstrated the authenticity and reliability of the ancient DNA data. The length of the mitogenome was 16,357 bp, which contained 13 protein-coding genes, two transfer RNAs, two ribosomal RNAs, and one control region. The total base composition of the mitochondrial genome was 30.30% A, 27.06% T, 12.37% G, 21.30 C, and 8.97% missing data with an AT composition of 57.36%. A maximum-likelihood phylogenetic tree was recovered including other roe deer sequences under the TIM2+I+G4 model. The nucleotide diversity of ancient and modern Capreolus pygargus populations based on mitochondrial genomes was calculated separately. This study reveals the clade-specific geographical distribution and long-term genetic continuity of Chinese Siberian roe deer, provides molecular evidence for their ancient utilization at Xiaotangshan site, and highlights the urgency of wild animal genetic diversity protection and the value of combining ancient-modern molecular data for conservation.