Abstract
Solanum trilobatum L. is an important medicinal plant in traditional Indian system of medicine belonging to Solanaceae family. However, non-availability of genomic resources hinders its research at the molecular level. We have analyzed the S. trilobatum leaf transcriptome using high throughput RNA sequencing. The de novo assembly of 136,220,612 reads produced 128,934 non-redundant unigenes with N50 value of 1347 bp. Annotation of unigenes was performed against databases such as NCBI nr database, Gene Ontology, KEGG, Uniprot, Pfam, and plnTFDB. A total of 60,097 unigenes were annotated including 48 Transcription Factor families and 14,490 unigenes were assigned to 138 pathways using KEGG database. The pathway analysis revealed the transcripts involved in the biosynthesis of important secondary metabolites contributing for its medicinal value such as Flavonoids. Further, the transcripts were quantified using RSEM to identify the highly regulated genes for secondary metabolism. Reverse-Transcription PCR was performed to validate the de novo assembled unigenes. The expression profile of selected unigenes from flavonoid biosynthesis pathway was analyzed using qRT-PCR. We have also identified 13,262 Simple Sequence Repeats, which could help in molecular breeding. This is the first report of comprehensive transcriptome analysis in S. trilobatum and this will be an invaluable resource to understand the molecular basis related to the medicinal attributes of S. trilobatum in further studies.
Highlights
Solanum trilobatum L. is one of the important medicinal plants belonging to family Solanaceae, more commonly available in Southern part of India
A total of 136,220,612 raw reads were generated from Solanum trilobatum leaf transcriptome that accounts for about 35.4 GB of paired-end sequencing data
The main aim of our study was to analyze the transcriptome of Solanum trilobatum using Illumina high throughput sequencing platform
Summary
Solanum trilobatum L. is one of the important medicinal plants belonging to family Solanaceae, more commonly available in Southern part of India. A pilot study, on clinical efficacy of S. trilobatum and Solanum xanthocarpum, confirmed the usefulness of these herbs in bronchial asthma. An in-depth study of S. trilobatum transcriptome is needed for analysis and characterization of its functional genes. This would help to achieve large-scale production of drugs via molecular breeding, transgenic technology, and metabolic engineering. RNA Sequencing-based de novo assembly is a well-developed approach to understanding transcriptomes of non-model plants with limited genomic information. RNA-Seq is a cost-effective tool, offers much data with better coverage and sufficient sequence depth for de novo assembly of transcriptomes. We report the transcriptome from the leaf of Solanum trilobatum using high throughput next-generation sequencing for the first time. The high-quality reads were de novo assembled into unique transcripts, which were extensively evaluated and annotated to identify the putative pathways and genes responsible for its medicinal properties
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