How to determine whether a contig is sex-linked
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6.8 years ago
ecophylic ▴ 20

I have paired-end RADseq data from Illumina HiSeq4000 of ~250 individuals containing a mix of males and females (where the sex is known of each individual). I would like to try to identify which reads belong to Z(X) and W(Y) chromosomes (the specimens are butterflies). I could write some scripts to compare heterozygosity between the reads to get some idea of which are Z (females should always be homozygous; ZW), but I imagine someone has already done this. Can someone point me to a program or pipeline that does this?

Thanks,
Sean

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I know nothing about butterflies or insects, but can you simply map them to an available reference genome?

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Quote: "I know nothing about butterflies or insects"

I'm sure you know SOMETHING about insects :)

http://onlinelibrary.wiley.com/doi/10.1111/1462-2920.12883/abstract

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TIL of the ZW system (you made a typo, females should be heterozygous ZW). You can find a few articles online (http://biorxiv.org/content/biorxiv/early/2015/07/27/023358.full.pdf ), from 2015. They require parents+F1 data.

I saw another article, http://gbe.oxfordjournals.org/content/6/3/526.full. In the Material and Methods(Physical Locations of Genes and Dosage Compensation), the author say they identify sex chromosomes by orthology with the Z chromosome of Bombyx mori. They are doing a de novo assembly, like you I guess.

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Thanks cyril-cros for the links; females would be heterogametic and thus not heterozygous on the Z for all loci.

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Unfortunately there is no reference at the moment. However, I could map to the silkworm as another way to get some indication of what might be sex-linked.

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