Heterogametic reference genome

[monkfromouterspace]

Hi there, thanks for this awesome package! Fills our needs almost perfectly, and I'm excited to use it. My species of interest has a reference genome, but unfortunately it's of the heterogametic sex. Is it possible to configure findZX to use this as the reference, or should I still just assemble from reads of the homogametic sex?

Thank you

[hsigeman]

Hi,

Thanks, really happy to hear that you find it useful!

Using a heterogametic reference genome requires some extra work but it is possible to use one as well. Shortly, what you want to do is to firstly run the pipeline using this reference genome. Secondly, you identify the Y/W-linked scaffolds using these two files (non-normalized coverage and heterozygosity scores for each scaffold):

• results/howler_monkey_test_dataset/output/no_synteny/tables/diffHeterozygosity.chr.out
• results/howler_monkey_test_dataset/coverage/gencov.mismatch.0.0.out

Thirdly, you remove the Y/W-linked scaffolds from the reference genome and run the pipeline again. I actually did exactly this for a collaboration a few years back (https://doi.org/10.1186/s12864-022-08963-1) and it worked really well. The Supplementary Information in that paper have some information but email me if you want more details, or if you want me to take a look at the data.

Hanna

[monkfromouterspace]

Hi Hanna,

Thanks so much for your help with this! I’m trying it for a species with homomorphic sex chromosomes so I’m interested to see how well it works.

Closing for now, but I’ll let you know how it goes! Thanks!!