Is it possible that *.a_ctg.gfa represents sex chromosome?

[Jung19911124]

Hi,

I ran Hifiasm on Hifi reads derived from an inbred strain of XX/XY species. In order to determine Y chromosome sequences, I extracted genomic DNA from male.

The result file, *.p_ctg.gfa, included some fragments, which are not found in reference assembly derived from female (XX individual). Those fragments must be linked to Y chromosome, but total length of the fragments was much smaller than I expected.

Then I realized *.a_ctg.gfa also consists of the small fragments which are not found in the female genome, and have a reasonable length for Y chromosome.

Is it possible that *.a_ctg.gfa represents heterogametic sex chromosome when we used an inbred strain?

Any advice would be appreciated. Best,

Jung

[chhylp123]

Yes, it is possible and it also depends on how large the Y chromosome is.

[Jung19911124]

Dear chhylp123,

Thank you for the reply. My species is an insect, so chromosome size is relatively small. Y chromosome of this species is estimated to be < 40 Mbp.