Entering edit mode
7.5 years ago
rajeshkumar_vinod
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30
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.
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.