Handling cultivars in transcriptome de novo assembly

Question

[DaneLukin]

Hi, i have to analyze expression data from two plant cultivars in three conditions. I wonder which is the correct way to create the de novo assembly which will be used a template. Should i merge all the samples and create a consensus assembly, or should i assembly them separately?, I have seem both methodologies published, which makes me a bit confused in the way to proceed. Any information is much appreciated.

Kind regards.

[h.mon]

Although I never seen, nor can provide, a good criterion, I guess the best approach will depend on the genetic similarity between the cultivars. Maybe you should do both strategies, then examine which one provides a better reference for the differential expression analysis.