There are many publications related to your task. Like :
Powell J. J. et al. The defence‐associated transcriptome of hexaploid wheat displays homoeolog expression and induction bias //Plant biotechnology journal. – 2017. – Т. 15. – №. 4. – С. 533-543. or
Chandra S. et al. De novo assembled wheat transcriptomes delineate differentially expressed host genes in response to leaf rust infection //PLoS One. – 2016. – Т. 11. – №. 2. – С. e0148453.
Don't you feel that you should try doing reference work by your self rather than getting it done from somebody else? Anyway here is an article which might help. Do not go by the title, read the entire article and it will answer your question.
of course you can....there are various second generation and third generation sequence techniques that can help you in your study, like whole genome sequencing, exome sequencing and so on. Your question is very generic. Please frame the question properly that will help you in deciding the appropriate sequencing system and also in literature review