chromosomal level assembly for sex chromosome

[zhxh233]

Hi @tangerzhang, I am wondering about using https://github.com/tangerzhang/ALLHiC/wiki/ALLHiC:-scaffolding-of-a-simple-diploid-genome to assemble the sex chromosome (2N=60, 58+XY). In your past answers, I prefered k=60 (or more than 60) in my command, but if my X chromosome and Y chromosome shared 80% sequence, would this command get (near) complete X and Y as different group in my final result ? Would you give me some advice for sex chromosome assembly ? Thank you.

[tangerzhang]

Hi @zhxh233 , I do not think the link you posted could solve the assembly of sex chromosomes. If you are working on the sex chromosomes, I suggest you can sequence male and female samples, then use these re-sequencing reads to dig out X-specific and Y-specific reads. These reads can be separately assembled into X and Y chromosomes. This is how we assembled X and Y chromosomes in Ficus hispida (Zhang et., al 2020 Cell). There are also alternative ways to achieve this goal. Below are some publications that may be helpful to your project: https://github.com/makovalab-psu/DiscoverY https://www.biorxiv.org/content/10.1101/2020.05.25.115592v1.full https://www.science.org/doi/10.1126/science.1257225?url_ver=Z39.88-2003&rfr_id=ori:rid:crossref.org&rfr_dat=cr_pub%20%200pubmed