Hello everyone, I have two plant varieties one is susceptible other one is resistant to virus infection. i want to do RNA-seq based analysis to find genes involved in host defense the problem is i do NOT have sequenced genome of those two varieties but genome of a third variety from same plant species is sequenced. Things i would like to do are finding novel gene discovery using cufflinks RABT based assembly and other genes involved in defense.
can i use this genome as a reference to analyze RNA-seq data of those two other plant species?
i think other approach which i can use is de-novo transcriptome assembly of those two plant varieties.