Is It Possible To Perform Synteny Study Between A Transcriptome And Genome Of Closely Related Species?

Question

[alok.helix]

Is it possible to perform synteny study between a transcriptome and genome of closely related specie?? will it be feasible given the speciation events that plants undergo. If it is possible, which tools need to be used?

[Michael]

I think, it can't be done, because the transcriptome is fragmented and you will get little if any information of gene order out of it. Maybe, one could think of calling variants from the RNA-seq (recycling the data) and thereby determine genetic distance of genes, but I also assume there are much more reliable techniques to achieve this (e.g. DNA sequencing).

[gammyknee]

Gene order would be colinearity rather than synteny. But you're right, it would be difficult to know precisely where a gene from a transcriptome is without locational information. A lot of people however have still done this study in plants, where a whole genome isn't feasible. It basically relies on the best match between a transcript and the closely related species. Its quite useful to study gene families

[alok.helix]

Thank you for the advice