Can you please tell me with reasons on how challenging it is to sequence heterozygous tetraploid potatoes with respect to its allelic diversity? Does 454 deep sequencing effectively help in assessing allelic diversity of heterozygous tetraploids? Is there any drawback of this method to the best of your knowledge in doing so?
I assume here that you want to use transcriptomic reads. If it's genomic reads I'm even more pessimistic. If there are specific genes that you want to target, the situation could be different.
I'm pessimistic, sorry to say. It will be hard to tell similar allelic variants apart. Also if you have something that you believe are allelic variants in your output the variants may instead be the result of gene duplications. Much depend on if you have a proper genome annotation of a tetraploid potato, which I doubt you have. Then you could map your reads instead of making a de novo assembly.
In any circumstance, if you have the choice, use Illumina. It's a lot cheaper and the data is much easier to work with.
Good luck in any case!
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