Question: How to identify a species is autopolyploid or allopolyploid by high-throughput sequencing?
0
gravatar for xzpgocxx
3 months ago by
xzpgocxx0
xzpgocxx0 wrote:

Hi,

I want to begin a genome project and firstly I need to know whether its an autopolyploid or allopolyploid.

The ploidyNGS can be used for exploring ploidy levels from NGS data, but not for identity autopolyploid or allopolyploid.

So, Is there some way can identify a species is autopolyploid or allopolyploid by using Illumina or PacBio reads?

Any help is much appreciated.

Thanks.

Best regards,

ADD COMMENTlink modified 3 months ago by Vitis2.1k • written 3 months ago by xzpgocxx0
1

define your terms please? sounds like an interesting problem, but I'm not familiar with the classes auto/allo polyploidy. A quick google looks like these phrases refer to the ancestry of the multi-copy genome in your sample. Do you know the ancestry of the mouse? It doesn't sound like something a toolkit processing NGS data is going to be able to answer for you. You'd need to reconstruct the phylogeny of the sample.

ADD REPLYlink modified 3 months ago • written 3 months ago by karl.stamm3.4k
2
gravatar for Vitis
3 months ago by
Vitis2.1k
New York
Vitis2.1k wrote:

The difference between autopolyploidy and allopolyploidy lies in the evolutionary distances between the ancestral genomes. For autopolyploids, the two copies of the genomes came from the same species or even the same individual. So the subgenomes are expected to be very similar. The only way to distinguish autopolyploidy and regular diploidy would probably be querying the allele frequencies of variants detected. If substantial deviation from 0.5 (heterozygosity in regular diploid organisms) is observed, it could indicate possible autopolyploidy. It should be noted the pattern has to be global, because local copy number variations generate similar deviations from heterozygosity, too.

For allopolyploids, I'd apply the same principle of allele frequency deviation, but expect much more differences between ancestral genomes. It becomes really tricky, because fixed differences between two ancestral genomes now look identical with regular heterozygous variants in a diploid. For selfing species, an elevated level of heterozygosity may indicate possible allopolyploidy, while for outcrossing species, you may need to estimate the overall variation level, an increasing level of overall variations, combined with deviation from 0.5 allele frequency would suggest possible allopolyploidy. The good news is that divergence outside genic regions increases very fast following speciation. Combining two genomes separated a couple millions years ago to form an allopolyploid would give you a lot of highly divergent regions outside genes. You may be able to find signatures of such regions from your data.

ADD COMMENTlink written 3 months ago by Vitis2.1k
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