Genome-wide analysis of methyl jasmonate-regulated isoform expression in the medicinal plant Andrographis paniculata

•Intron retention (IR) isoform expression is regulated when plants are facing environmental stress.•Single-molecule real-time (SMRT) sequencing can capture full-length isoform transcripts.•The number of IR isoforms down-regulated after methyl jasmonate (MeJA) treatment was more than double that of up-regulated IR isoforms.•Four IR isoforms showed significant differential expression after MeJA treatment.