I'm working on genes involved in Biosynthetic Pathway of Pachymic Acid in Wolfiporia Cocos. We have transcriptomic data. But in that data the genes probably involved in the synthesis of Pachymic are not clear. So is there any method to find out the gene?
*Note Further more we want to check gene expressions on different treatment levels.
You can perform standalone BLAST for your assembled transcriptome data against the NR database. This will give you the transcripts corresponding to the pathway genes, provided you have pathway genes known in other species. You can fetch out your pathway specific genes, even full length genes after overlapping the transcripts.
Follow the paper for same: https://www.sciencedirect.com/science/article/abs/pii/S0141813019402171
It is most surely produced by one of the steroid producing enzymes. Do an MS and mRNA sequencing from plant tissue and identify all steroid producing enzymes. Then use bioinformatic tools to clear out enzymes with known products and to predict which one would be able to create your product. Then you need to confirm your findings in vitro.
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