De novo transcriptome analysis and comparative expression profiling of genes associated with the taste-modifying protein neoculin in Curculigo latifolia and Curculigo capitulata fruits

Abstract

Background Curculigo latifolia is a perennial plant found in Southeast Asia whose fruits contain the taste-modifying protein neoculin, which binds to sweet receptors to make sour fruits taste sweet. Although neoculin is similar to Galanthus nivalis agglutinin (GNA), which contains mannose-binding sites in its sequence and 3D structure, neoculin lacks such sites and has no lectin activity. Whether the fruits of C. latifolia and other Curculigo plants contain neoculin and/or GNA family genes is unclear. Results We performed de novo RNA-seq assembly of the fruits of C. latifolia and the related C. capitulata and analyzed the expression patterns of neoculin and neoculin-like genes in both species in detail. We assembled 85,697 transcripts from C. latifolia and 76,775 from C. capitulata using Trinity and annotated them using public databases. We identified 70,371 unigenes in C. latifolia and 63,704 in C. capitulata. In total, 38.6% of unigenes from C. latifolia and 42.6% from C. capitulata shared high similarity between the two species. We identified ten neoculin-related transcripts in C. latifolia and 15 in C. capitulata. Genes encoding both the basic and acidic subunits of neoculin were present in both plants. We aligned these 25 transcripts and generated a phylogenetic tree. Many orthologs in both species shared high similarity, despite the low number of common genes, suggesting that these genes likely existed before the two species diverged. The relative expression levels of these genes, as indicated by their transcript per million (TPM) values, differed considerably between the two species: the TPM values of neoculin genes were 60 times higher in C. latifolia than in C. capitulata, whereas those of GNA family members were 15,000 times lower in C. latifolia than in C. capitulata. Conclusions The genetic diversity of the neoculin-related genes strongly suggests that neoculin genes underwent duplication during evolution. The marked differences in the expression profiles of neoculin-related genes between C. latifolia and C. capitulata could be due to mutations in regions involved in transcriptional regulation. Comprehensive analysis of the genes expressed in the fruits of these two Curculigo species helped elucidate the origin of neoculin at the molecular level.