PRJDB2442
Transcriptomic landscape of Pueraria lobata demonstrates potential for phytochemical study
In this study, more than 93 million fastq format reads were generated by Illumina’s next-generation sequencing approach using five types of P. lobata tissue, followed by CLC de novo assembly methods, ultimately yielding about 83,041 contigs in total. Then BLASTx similarity searches against the NCBI NR database and UniProtKB database were conducted. Once the duplicates among BLASTx hits were eliminated, ID mapping against the UniProt database was conducted online to retrieve Gene Ontology (GO) information. By mapping the reads back to contigs, RPKM (reads per kilobase of the transcript per million mapped reads) values were calculated to demonstrate gene expression levels for five tissues, and overrepresented GO terms were evaluated using Fisher’s exact test. In search of the putative genes relevant to essential biosynthesis pathways, all 1,348 unique enzyme commission numbers (EC) were used to map pathways against the Kyoto Encyclopedia of Genes and Genomes (KEGG). Enzymes related to the isoflavonoid and flavonoid biosynthesis pathways were focused for detailed investigation. Adopting RNA-Seq analysis, we obtained substantially credible contigs for downstream work. The findings in this report may serve as a footstone for further research into this promising medicinal plant.