A telomere-to-telomere genome assembly of Chinese water deer (Hydropotes inermis)

Hydropotes inermis (Chinese water deer, 2n = 70) is a relatively primitive small Cervidae species naturally distributed along the eastern coast of China and the Korean Peninsula. High-quality genomic resources are essential for investigating its unique adaptive and biological traits. In this study, we assembled the telomere-to-telomere (T2T) gap-free genome of a female H. inermis using PacBio HiFi, Oxford Nanopore Technologies (ONT), and Hi-C sequencing technologies. The assemblies were 3.45 Gb with a contig N50 of 101.09 Mb in size, which were anchored on 35 chromosomes, carrying 60 telomeres and 35 centromeres. Genome annotation annotated 33.36% repetitive sequences and 24,398 protein-coding genes. Comparative analyses with genomes of closely related species confirmed high genome integrity, continuity, and accuracy, supported by a quality value (QV) of 52.56 and a BUSCO completeness of 99.40%. This study provides a valuable genetic resource for H. inermis and serves as an important reference for investigating the evolutionary history of Cervidae.