Chromosome-Level Genome Assembly for the Chinese Serow (Capricornis milneedwardsii) Provides Insights Into Its Taxonomic Status and Evolution

Abstract

Chinese serow (Capricornis milneedwardsii) is mainly distributed in the south of Yellow River in China, which has been listed as vulnerable by the International Union for Conservation of Nature (IUCN). However, the reference genome of serow has not been reported and its taxonomic status is still unclear. Here, we first constructed a high-quality chromosome-level reference genome of C. milneedwardsii using PacBio long HiFi reads combined with Hi-C technology. The assembled genome was ~2.83 Gb in size, with a contig N50 of 100.96 Mb and scaffold N50 of 112.75 Mb, which were anchored onto 24 chromosomes. Furthermore, we found that the Chinese serow was more closely related to muskox, which diverged from ~4.85 million years ago (Mya). Compared to the karyotype of goat (2n = 60), we found the Chinese serow (2n = 48) experienced six chromosome fusions, which resulted in the formation of six central centromere chromosomes. We also identified two positively selected genes (MYH6 and DCSTAMP) specific to Chinese serow, which were involved in 'viral myocarditis' and 'Cardiac muscle contraction'. Interestingly, compared to other Caprinae animals, the MYH6 protein of Chinese serow occurred two mutations (E1520S and G1521S), which might be related to hypoxia tolerance. The high-quality reference genome of C. milneedwardsii provides a valuable information for protection of serows and insights into its evolution.

Keywords: Chinese serow; HiFi; Hi‐C; chromosomal evolution; hypoxia tolerance.

FIGURE 1

Chinese serow in Qinling Mountains (Photographer: Naxun Zhao).

FIGURE 2

Overview of C. milneedwardsii genome assembly. (A) The Hi‐C interaction heatmap of Chinese serow. (B) Circos plot showing the visualization of genomic details with a window of 1 Mb. a. gene density; b. repeat content; c. GC content. (C) The contig N50 and the number of gaps of different domestic and wild animals. (D) The ratio of repeat sequences in Chinese serow genome.

FIGURE 3

Phylogenetic and chromosomal evolution analysis. (A). Phylogenetic analysis at the genomic level. (B) The collinear relationship of Takin, Goat and Chinese serow.

FIGURE 4

The two mutations of MYH6 protein in Chinese serow. (A) The two mutations of E1520S and G1521S in Chinese serow was different from other Caprinae animals; (B) Changes in 3D structure before and after mutations; (C) Changes in hydrophobicity before and after mutations. Light blue color: 1520aa; Light green color: 1521aa; Red color: The hydrogen bond between the two α‐helices; Yellow color: The hydrogen bond.