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I've done some transcriptomics work in the past with a polyploid organism, and this presented some unique challenges in the data processing and analysis. Since then, I have been brainstorming about the technical challenges one may face when sequencing and assembling the genomes of a polyploid organism. As far as I am aware, there are no polyploids whose genomes have been sequenced.

If one wanted to sequence, for example, a tetraploid organism, one approach would be to prepare and sequence all of the DNA together and then rely on post-sequencing analysis to tease apart the two co-resident genomes. However, it would be difficult, if not impossible, with this approach to distinguish inter-genome variation from intra-genome variation.

An alternative approach would be to isolate DNA from both co-resident genomes separately, and then sequence and assemble the genomes separately, so that inter-genome variation and homology need not be considered. However, I'm thinking at a very high level and have little intuition as to the technical feasibility of this approach. When there are two or more co-resident genomes, is it be possible to isolate DNA from only one of those genomes? What would this rely on (for example, would thorough cytogenetic/cytogenomic characterization help)? If this task is not possible, what types of limitations must be overcome to enable it?

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  • $\begingroup$ I'm interested in the issues related to transcriptomics on polyploid organisms (I'll be doing some comparative transcriptomics between related but different ploidy organisms). If I ask this as a separate question, could you elaborate on the issues involved and how you solved them? $\endgroup$
    – Rik Smith-Unna
    Feb 18, 2012 at 19:08
  • $\begingroup$ I'm not sure, as the material is yet unpublished. I guess it would depend on the question. $\endgroup$
    – Daniel Standage
    Feb 20, 2012 at 12:03
  • $\begingroup$ @jmusser I reverted your title edit since it didn't really capture the question. The title "How are the genomes of polyploid organisms sequenced?" isn't really appropriate--it seems like you're asking how it is currently done (it's not). I'm asking how it should or could be done. If you have any more suggestions about improving the title, I'd be happy to consider these. $\endgroup$
    – Daniel Standage
    Feb 22, 2012 at 14:20
  • $\begingroup$ @DanielStandage, sorry, I just like to turn the title into a question. :) $\endgroup$
    – J. Musser
    Feb 22, 2012 at 14:33
  • $\begingroup$ @jmusser No worries, I have no problem with that assuming question adequately captures what is being asked. $\endgroup$
    – Daniel Standage
    Feb 22, 2012 at 14:50

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Take a look at the strategies used to sequence the wheat genome. Wheat is hexaploid. The project is described at http://www.wheatgenome.org/.

For early work on the maize genome, we employed methyl filtration in order to reduce genome complexity and size - transposons are filtered out and genes + promoters and such remain. The gene sequences are different from the two genomes, so says the theory, and those can be distinguished. See http://www.ncbi.nlm.nih.gov/pubmed/10545948 for the reference.

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  • $\begingroup$ As I know wheat (both 4n and 6n) is allpolyploid (it came into being by hybrydization of different species). Isn't it harder to sequence genome of autopolyploid species? $\endgroup$
    – Marta Cz-C
    Feb 23, 2012 at 9:30
  • $\begingroup$ I'm not sure. Sequencing is not the real problem - it is accurate genome assembly. $\endgroup$
    – Larry_Parnell
    Feb 23, 2012 at 17:59

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