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Location of centromere

Hi,

I am looking to find a way to locate centromeres in a genome assembly.

Any recommendations ?

Thanks for your help.

genome centromere
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written by Picasa Picasa

Is it something well-annotated like human/mouse/fly/worm or a complete de novo assembly?

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written by ATpoint ATpoint

it's a complete de novo assembly of non model organism.

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written by Picasa Picasa

I don't expect your assembly actually includes the centromere. Did you use long reads? How many scaffolds do you have and how many chromosomes do you expect?

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written by WouterDeCoster WouterDeCoster

Yes it's a PacBio assembly at contig level (around 10k contigs). My species has 12 pairs of chromosomes.

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written by Picasa Picasa

Then chances are that your contigs are broken at the centromeres and do not span those.

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written by WouterDeCoster WouterDeCoster

could you give more explanation please ?

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written by Picasa Picasa

2 answers

Centromeres are long and repetitive. Assembly across long and repetitive sequences is hard.

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written by WouterDeCoster WouterDeCoster

Also not easily sequenceable with current technologies we have. See this.

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written by GenoMax GenoMax

What have you tried so far? A quick google search brings up a couple of articles that seem to address the assembly of centromeres in different species: Drosophila, Grey Mouse Lemur, Human, Bovidae

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written by Friederike Friederike

Thanks for the papers ! , I will take a look.

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written by Picasa Picasa

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