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.