Location of centromere

Question

[Picasa]

Hi,

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

Any recommendations ?

Thanks for your help.

[ATpoint]

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

[Picasa]

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

[WouterDeCoster]

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?

[Picasa]

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

[WouterDeCoster]

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

[Picasa]

could you give more explanation please ?

Answer 1

[WouterDeCoster]

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

[GenoMax]

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

Answer 2

[Friederike]

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

[Picasa]

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