4.1 High-quality chromosome-level assembly reference genome of takin
The genome size of takin was about 2.95 Gb, which was slightly larger than that of the cattle (~2.72 Gb) (Rosen et al. 2020), goat (~2.70 Gb) (Li et al. 2021) or sheep (~2.63 Gb) (Davenport et al. 2021). The contig N50 of takin assembly genome reached 68.05 Mb, which was also larger compared to cattle (~25.90 Mb), goat (~46.21 Mb) and sheep (~43.18 Mb). Moreover, the takin assembly genome, which only has 151 gaps, had a good collinearity relationship with goat and sheep. Further, Hi-C reads with a N50 of 101.27 Mb were anchored onto 25+XY chromosomes. These results showed a high-quality chromosome-level reference genome of takin was assembled. 49.48% of reference genome was repeat sequences. Among these repeat sequences, 554,037 SSRs were identified which were more than that of the takin transcriptome (Qiu et al. 2021). These SSRs could be used as molecular markers for population genetic analysis and conservation of takins.
4.2 Taxonomic status and chromosome evolutionof takin
The mitochondrial genome was assembled from HiFi reads, which showed high similarity with that of the GenBank database. The HiFi reads can reach to an average length of 14 kb, thus the assembled mitochondrial genome was highly credible. Phylogenetic results of subfamily Caprinae showed that takin was closely related to goat and Bharal at the mitochondrial genome level. However, it was more closely related to muskox at the genomic level. It indicated that mitochondrial evolution is different from genome evolution. Previous studies showed that takin was most closely related to goat (Feng et al. 2016, Kumar et al. 2019, Zhou et al. 2019) at the mitochondrial genome level, which was consistent with the present study. However, based on the morphology, ecological traits and G-banded karyotype, takin showed similarity to muskox (Pasitschniak-Arts et al. 1994). Combined with the phylogenetic analysis at the genomic level, we speculated that it is more reasonable to classify takin and muskox into subfamily Ovibovini.
Chromosome evolution is linked to phenotypic evolution, gene family evolution and speciation (Eichler and Sankoff 2003, Damas et al. 2021). In the Bovidae family, the number of chromosomes dramatically varied in case of cattle (2n=60), goat (2n=60), sheep (2n=54), takin (2n=52) and muskox (2n=48). Based on the chromosome-level reference genome in muskox, the ancestral karyotype (2n=60) was reconstructed with cattle, goat, sheep and takin. The karyotype of takin (2n=52) occurred when there were four chromosome fusions and one translocation from the ancestor (2n=60). As a result, the number of chromosomes in takin has been reduced to 2n=52. Previous studies showed chromosome evolution was related to chromosome fission and fusion events (Chen et al. 2019, Liu et al. 2021, Yin et al. 2021). Interestingly, a functional single-chromosome yeast was successfully created by end-to-end chromosome fusions and centromere deletions (Shao et al. 2018). Therefore, further research on chromosome arrangements is required in the Bovidae family to reveal the relation of chromosome evolution as well as rapid evolution of genomic sequences.