Transcriptome Sequencing of Lepisanthes Fruticosa to Discover SSR Markers

Abstract

Lepisanthes fruticosa (ceri Terengganu) is one of the important underutilized fruit plants with high value of bioactive compounds and pharmacological properties. Current studies have focused mainly on the bioactive compounds which are essential for functional food and pharmaceutical applications. However, studies on the diversity and conservation of L. fruticosa are still scarce since genomic and genetic resources for this plant species are still lacking. In this study, RNA sequencing of L. fruticosa leaf was carried out using Illumina HiSeq to identify potential unigenes and simple sequence repeats (SSRs). A total of 52,657 unigenes were identified from about 91,043,356 million raw sequence reads. Mining of SSRs from these unigenes have predicted a total of 23,958 SSRs which was approximately 45.58% of total unigenes obtained. Dinucleotide repeats motif was the highest (21.48%) and the next were trinucleotide repeats motif (14.65%). A total of 4,620 SSRs ranging from 12 to 116 bp were selected for experimental validation. Bioinformatic analysis via GO and KEGG platforms showed that a total of 1,861 (40.28%) SSR-containing unigenes matched to Gene Ontology (GO) terminology and 48 biochemical pathways. The SSR-containing unigenes of L. fruticosa were involved in various cell functions and a majority of their functions were associated with purine and thiamine metabolism. In addition. A majority of SSR-containing unigenes were involved in organic and heterocylic compounds bindings, indicating an active event of biosynthesis process of secondary metabolites in L. fruticosa. SSR markers obtained from this study provides new genetic information that can be utilized to facilitate future characterization of L. fruticosa accessions at molecular levels.