RNA-Seq analysis of bitter gourd fruit transcriptome identifies mature seed-specific expression of Momordica charantia unknown protein 1 (McUNP1) gene and its association with intron retention

Bitter gourd (Momordica charantia L.) is an important vegetable crop widely used in traditional medicine for the management of diabetes. However, molecular studies in this crop are limited. Initially, we analyzed the transcriptome of different tissues within the bitter gourd fruit. Based on the fragments per kilobasemillion (FPKM) values, we identified 2300, 4365, 2948, 6042, and 15,131 transcripts that were expressed only in green rind, white rind, pulp, immature seeds, and mature seed, respectively. Out of the 15 transcripts that were screened by reverse transcription-polymerase chain reaction (RT-PCR), only two (13%) were found to be specific to the tissues within the fruits. One transcript was specific to the green rind, while the other was specific to mature seeds. The transcript from mature seeds was tissue-specific at the whole plant level as well. This transcript contained five exons and four introns and coded for an unknown protein, McUNP1. A comparison of the RNA and DNA sequences revealed that the expression of the McUNP1 gene included a fully spliced RNA and an alternatively spliced RNA that retained the intron 4 (McUNP1-int4). Quantitative RT-PCR (qRT-PCR) analysis confirmed tissue-specific expression of the McUNP1 gene in mature seeds. The RNA with intron retention (IR) accounted for approximately 83% of McUNP1 gene expression in mature seeds. The functional importance of the McUNP1 gene and IR during its expression remains unknown. This is the first report of intron retention and its association with tissue-specific gene expression in bitter gourd.