Question About Lack of Synteny in Scaffold_1

[zixueli57-wq]

Dear Professor,
I would like to ask for your advice regarding an issue I encountered. In the HapHiC visualization, I aligned my assembled genome to a closely related species using minimap2. The results show that scaffold_1 exhibits almost no synteny with the corresponding genome of the related species.
It is worth noting that the individual I am studying is male, but scaffold_1 is not part of the Y chromosome.
Could you please help me understand the possible reasons for this lack of synteny?

[zengxiaofei]

You can try running a BLAST search of the scaffold_1 sequences against the nt database to see what species they might be from.