I am working on a plant containing six homologous sets of chromosomes，now I want to explore the different gene expression of two period in same tissue, but I don't know whether should I do a RNA sequencing? The plant also have a wild type,is a diploid, and its whole genome has been published.
Thank you for your attention!
You should do RNA-Seq. Even if its genome is not yet sequenced it's possible to study transcriptome using de-novo assembly (Trinity). In addition, you can study mRNA + lncRNA. However you should read a little bit the litterature and exactly design your experiment before sequence anything. Depending on what your are looking, sequencing depth and/or multiple biological replicates might be very important.
If you want to look at differential gene expression, you basically have to do RNA-seq for most organisms. As far as I know, the alternatives, like qPCR, are only applicable to highly-studied organisms such as mouse and human.
In my understanding, qPCR can be done if you can make primers for the transcripts. So you don't absolutely need the genome even. For example in the salmon louse, qPCR was done based on EST sequences and clones long before we had the genome. Certainly, the primer design would benefit from having the whole genome, but it's not absolutely necessary.
I should clarify that I was under the impression not that qPCR is impossible for some random organism, but that RNA-seq is so much cheaper than designing and producing custom primers for thousands of transcripts that qPCR becomes cost-prohibitive unless you want to do it on a large scale. RNA-seq will be on the order of a few thousand dollars. But, I am not familiar with qPCR pricing... perhaps you can give a ballpark figure for running it on a new organism, or on an organism with a mass-produced kit?
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what is "two period"? did you mean two genes or two stages? If you only want to measure a few genes, qPCR is indeed an options.
Two different stages, and I wanted to find the different expression genes between two stages.