The assembly of caprine Y chromosome sequence reveals a unique paternal phylogenetic pattern and improves our understanding the origin of domestic goat

The mammalian Y chromosome offers a unique perspective on the male
reproduction and paternal evolutionary histories. However, further
understanding of the Y chromosome biology for most mammals is hindered by
the lack of a Y chromosome assembly. This study presents an integrated in
silico strategy for identifying and assembling the goat Y-linked scaffolds
using existing data. A total of 11.5 Mb Y-linked sequences were clustered
into 33 scaffolds, and 187 protein-coding genes were annotated. We also
identified high abundance of repetitive elements. A 5.84 Mb subset was
further ordered into an assembly with the evidence from the goat
Radiation-Hybrid map (RH map). The existing whole-genome re-sequencing
data of 96 goats (worldwide distribution) were utilized to exploit the
paternal relationships among bezoars and domestic goats. Goat paternal
lineages were clearly divided into two clades (Y1 and Y2), predating the
goat domestication. Demographic history analyses indicated that maternal
lineages experienced a bottleneck effect around 2,000 YBP (years before
present), after which goats belonging to the A haplogroup spread worldwide
from the Near East. As opposed to this, paternal lineages experienced a
population decline around the 10,000 YBP. The evidence from the Y
chromosome suggests that male goats were not affected by the A haplogroup
worldwide transmission, which implies sexually unbalanced contribution to
the goat trade and population expansion in post-Neolithic period.