Question: Sequence and assemble polyploid genome ?
1
gravatar for Picasa
3.8 years ago by
Picasa480
Picasa480 wrote:

Currently genome assemblers is good for haploid samples, and provide also a haploid assembly for diploid genome.

1) What about polyploid genomes such as plants ? From what I understand, it's problematic because an assembly of polyploid genome could result of a chimeric genome ?

2) Does it exists an assembly which take account of polyploid genome.

3) What are the strategies used to sequence a polyploid genome ?

4) I'm not a biologist but I'm wondering if is it possible to isolate chromosomes from a sample and sequence it separately. Then assemble it by classical way.

I mean, for a triploid organism (for example in this figure) :

https://figures.boundless.com/21357/raw/-2ctriploid-and-tetraploid.svg

Isolate each chromosome, so we'll get 9 samples to sequence (3 for each chromosome) and assemble it separately.

polyploid assembly • 1.7k views
ADD COMMENTlink modified 3.8 years ago by Shyam130 • written 3.8 years ago by Picasa480
1
gravatar for mastal511
3.8 years ago by
mastal5112.0k
mastal5112.0k wrote:

Cortex is an assembler used for plant genomes.

http://cortexassembler.sourceforge.net/

Individual chromosomes have been isolated and sequenced for wheat. See for example

http://bmcgenomics.biomedcentral.com/articles/10.1186/1471-2164-15-1080

ADD COMMENTlink written 3.8 years ago by mastal5112.0k
0
gravatar for Picasa
3.8 years ago by
Picasa480
Picasa480 wrote:

Thanks.

Have you already used Cortex ?

ADD COMMENTlink written 3.8 years ago by Picasa480
0
gravatar for Shyam
3.8 years ago by
Shyam130
United States
Shyam130 wrote:

It is possible to isolate chromosomes separately using flow cytometry. In case of wheat they flow sorted the chromosomes based on size and evaluated the quality ie. presence of other chromosomes based on chromosome specific markers. Then they are sequenced using Hiseq. Abyss assembler was used for the assembly.

ADD COMMENTlink written 3.8 years ago by Shyam130
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