Question: Location of centromere
1
gravatar for Picasa
14 months ago by
Picasa540
Picasa540 wrote:

Hi,

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

Any recommendations ?

Thanks for your help.

centromere genome • 388 views
ADD COMMENTlink modified 14 months ago • written 14 months ago by Picasa540

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

ADD REPLYlink written 14 months ago by ATpoint38k

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

ADD REPLYlink written 14 months ago by Picasa540

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 14 months ago by WouterDeCoster44k

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

ADD REPLYlink written 14 months ago by Picasa540

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

ADD REPLYlink written 14 months ago by WouterDeCoster44k

could you give more explanation please ?

ADD REPLYlink written 14 months ago by Picasa540
0
gravatar for WouterDeCoster
14 months ago by
Belgium
WouterDeCoster44k wrote:

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

ADD COMMENTlink written 14 months ago by WouterDeCoster44k

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

ADD REPLYlink modified 14 months ago • written 14 months ago by genomax89k
0
gravatar for Friederike
14 months ago by
Friederike6.0k
United States
Friederike6.0k 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 14 months ago by Friederike6.0k

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

ADD REPLYlink modified 14 months ago • written 14 months ago by Picasa540
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