Question: Location of centromere
1
gravatar for Picasa
4 months ago by
Picasa480
Picasa480 wrote:

Hi,

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

Any recommendations ?

Thanks for your help.

centromere genome • 233 views
ADD COMMENTlink modified 4 months ago • written 4 months ago by Picasa480

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

ADD REPLYlink written 4 months ago by ATpoint26k

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

ADD REPLYlink written 4 months ago by Picasa480

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?

ADD REPLYlink written 4 months ago by WouterDeCoster42k

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

ADD REPLYlink written 4 months ago by Picasa480

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

ADD REPLYlink written 4 months ago by WouterDeCoster42k

could you give more explanation please ?

ADD REPLYlink written 4 months ago by Picasa480
0
gravatar for WouterDeCoster
4 months ago by
Belgium
WouterDeCoster42k wrote:

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

ADD COMMENTlink written 4 months ago by WouterDeCoster42k

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

ADD REPLYlink modified 4 months ago • written 4 months ago by genomax75k
0
gravatar for Friederike
4 months ago by
Friederike5.2k
United States
Friederike5.2k wrote:

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

ADD COMMENTlink written 4 months ago by Friederike5.2k

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

ADD REPLYlink modified 4 months ago • written 4 months ago by Picasa480
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