Is It Possible To Perform Synteny Study Between A Transcriptome And Genome Of Closely Related Species?
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?
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Istvan Albert
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alok.helix
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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).
Thank you for the advice
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