To know if genome of a plant variety from same species can be used to analyze RNA-seq data of other variety of same plant
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.
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Can you further clarify "variety"? Are these plants cultivars of the same species?
yes they are same species genome sequence of following varieties are available on internet http://peppersequence.genomics.cn/page/species/index.jsp but i have to use a pathogen resistant variety of chilli for which i want to find differentially expressed genes during pathogen infection.
thank you
It is not uncommon to use closely related species as a reference in plants. Offcourse the divergence can not be very high. I can state two example of papers here and second one in Maize Hapmap2 project where a closely related species tripsacum reads where aligned to maize. In the first case cultivated tomato genome was used as a reference to align reads from solanum chilense and Solanum peruvianum both of which have a few million years divergence. But for genes involved in pathogen resistance (like Rgenes) one has to be more careful due to profuse rearrangements and shuffling even or short timescales. I am sorry that I can not suggest any mappers/parameters/pipelines as I have not done it myself but most of these studies use near default params. My guess would be to attempt both a)mapping to a close reference b) de-novo assembly of samples separately given a high number of reads. House_keeping/Stably_expressed genes could give an indication of the bias as they should not differ much and params can be tuned accordingly.