Comprehensive transcriptome analysis of Lactuca indica, a traditional medicinal wild plant

Abstract

Lactuca indica Linn. (Indian lettuce) is an undomesticated, traditional medicinal plant belonging to the Compositae family. Here, we performed transcriptome assembly and functional annotation of this medicinal plant, along with secondary metabolite analysis. Sesquiterpene lactones, the most abundant secondary metabolites in Lactuca species, are mainly responsible for the medicinal properties of Lactuca. We therefore measured the levels of lactucin, a primary sesquiterpene lactone, in 61 accessions of L. indica, which varied from 1.9 μg/g to 98.7 μg/g. De novo transcriptome assembly yielded 73,300 unigenes from 127 million reads based on 12.9 Gb of data. In total, 28,970 and 34,519 unigenes were annotated using the Swiss-Prot and TAIR10 databases, respectively. The most highly enriched Gene Ontology term for these unigenes was metabolic processes. Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis identified 97 significant pathways; the top two pathways were metabolic pathways and biosynthesis of secondary metabolites. Among the 9743 unigenes mapped to 97 significant KEGG pathways, 52 complete unigenes encoding 23 key enzymes in the terpenoid backbone pathway were identified. We identified 1685 transcription factor genes belonging to 53 families and 8830 simple sequence repeat (SSR) loci based on the transcripts. The high-quality transcriptomic and metabolic data on this indigenous herb obtained in this study represent a valuable genetic resource for breeding an L. indica cultivar with excellent pharmaceutical benefits.