vertebrate sex chromosomes

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Nayden Chakarov

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Nov 8, 2020, 11:39:01 AM11/8/20
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Hi Olga and Neva,
sorry if I've missed a thread on this, but Is there a classic correct way to deal with defining boundaries of sex chromosomes which show partially duplicated sequences in JBAT? It seems that overlapping chromosome boundaries and copy/pasting to duplicate are not possible and would probably be harmful options for most uses.
I guess removing and adding chromosome boundaries and patching them together from two assembly definitions could work. Or go through the diploid.sh after the rather tedious production of vcf-files with gatk etc.
What would you recommend?
Nayden
2020.11.08.17.29.28.HiCImage.pdf

Olga Dudchenko

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Nov 8, 2020, 7:17:42 PM11/8/20
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I am sorry I am not sure I fully understand the question. It seems you are asking if there is a way to duplicate the sequence in JBAT? Unfortunately no, there isn't. You can still do it manually in the assembly file. We usually don't do it for DNA Zoo assemblies, assign the PAR to X (in mammal case) and just leave a note about the boundaries of PAR in the readme. -Olga

Nayden Chakarov

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Sep 17, 2021, 6:28:41 AM9/17/21
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Hi Olga, 
I did assemblies of two bird species but have problems interpreting the PAR region of one of them. It would be great if you could help!
In Buteo it is approximately as it should be : the Z ( similar to mammalian X) chromosome has ~ half the coverage of autosomes and there is a ~ 10 MB PAR region linking both to Z and W which has the added coverage of Z  and W. The W chromosome has somewhat lower coverage than Z. A colleague suggested that this might be due to higher repeat density and repeat filtering in the 3d scripts. Do you think/know that this happens?
In Pernis the region with added Z & W /approx. autosomal coverage/ is smaller - only ~ 2 MB (the one bigger contig around the 40 MB mark in the pic) but the potential PAR region linking to both probable sex chromomes is larger and does not have higher coverage than the non-PAR sex chromosome regions. Any ideas what could cause this?
Thanks,
Nayden 

Buteo_sex_chr.pdf
Pernis_sex_chr.pdf

Olga Dudchenko

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Sep 19, 2021, 12:44:08 AM9/19/21
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Hi Nayden,

It is hard to judge from a static image. My guess would be that what you see as "linking" region in fact represents sequences that 1) are divergent enough for the contigger to dump both the Z and W sequences in Pernis (unlike Buteo where PAR bits the contigger assembles only once); at the same time 2) the sequences are similar enough that the aligner mixes Hi-C contacts up (or maybe your Hi-C is not from the same individual etc.), so that the corresponding regions end up having a high (false) contact frequency. As a result, they end up being scaffolded together, more or less corresponding bit in W after the corresponding bit in Z through much of that "linking" region. The higher coverage are the only PAR bits that actually the contigger spits out as a single sequence.

Best,
Olga
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