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.

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Background Justicia adhatoda is an important medicinal plant traditionally used in the Indian system of medicine and the absence of molecular-level studies in this plant hinders its wide use, hence the study was aimed to analyse the genes involved in its various pathways. Methods and results The RNA isolated was subjected to Illumina sequencing. De novo assembly was performed using TRINITY software which produced 171,064 transcripts with 55,528 genes and N50 value of 2065 bp, followed by annotation of unigenes against NCBI, KEGG and Gene ontology databases resulted in 105,572 annotated unigenes and 40,288 non-annotated unigenes. A total of 5980 unigenes were mapped to 144 biochemical pathways, including the metabolism and biosynthesis pathways. The pathway analysis revealed the major transcripts involved in the tryptophan biosynthesis with TPM values of 6.0903, 33.6854, 11.527, 1.6959, and 8.1662 for Anthranilate synthase alpha, Anthranilate synthase beta, Arogenate/Prephenate dehydratase, Chorismate synthase and Chorismate mutase, respectively. The qRT-PCR validation of the key enzymes showed up-regulation in mid mature leaf when compared to root and young leaf tissue. A total of 16,154 SSRs were identified from the leaf transcriptome of J. Adhatoda ,which could be helpful in molecular breeding. Conclusions The study aimed at identifying transcripts involved in the tryptophan biosynthesis pathway for its medicinal properties, as it acts as a precursor to the acridone alkaloid biosynthesis with major key enzymes and their validation. This is the first study that reports transcriptome assembly and annotation of J. adhatoda plant. Supplementary Information The online version contains supplementary material available at 10.1007/s11033-022-07784-5.

RNA Sequencing based de novo assembly is a well-developed approach in understanding transcriptomes of non-model plants with limited genomic information. RNA-Seq is cost effective tool, offers much data with better coverage and sufficient sequence depth for de novo assembly of transcriptomes. In past few years, there has been an increase in utilising RNA-Seq for discovery and identification of functional genes involved in the biosynthesis of active compounds in non-model plants. In this study, we analysed the transcriptome of Solanum trilobatum L. leaf using high throughput next generation sequencing. S. trilobatum is one of the important medicinal plants belonging to family Solanaceae and commonly available in South India. The studies conducted so far, to understand its therapeutic potential, have yielded positive results. Its extract is used to treat conditions like chronic bronchitis and tuberculosis. It is also reported to have anti-oxidative, hepatoprotective, anti-inflammatory, anti-microbial, antitumour activities. The total RNA from S. trilobatum leaf was isolated and sequenced using Illumina Hiseq 2500 platform with paired end chemistry. In total, 136,220,612 high quality sequence reads were obtained. The raw reads were pre-processed and assembled into 144,580 assembled transcripts using Trinity-a de novo assembler and clustering of transcripts was done using CD-HIT resulting 128,934 unigenes. The unigenes were extensively evaluated and annotated with various databases to identify pathways and genes responsible for biosynthesis of medicinal compounds. Based on similarity search with known proteins 60,097 (46.61% of all unigenes), 35,141 (27.25%), 30,427 (23.60%) and 61,986 (48.07%) had homologs in nr, Pfam, GO and UniProt databases respectively. The comparison against the KEGG database mapped 14,490 (11.23%) unigenes to 138 pathways, where flavonoid biosynthesis pathway was identified to be the highly represented. The expression levels of the transcripts were quantified using RSEM and Reverse Transcription PCR (RT-PCR) of few genes were performed to validate the transcriptome assembly. The SSRs and transcription factors, which could help for the molecular breeding, were also identified. This is the first report of complete transcriptome analysis in S. trilobatum. The genomic resources generated will serve as foundation to understand molecular basis of medicinal properties of S. trilobatum in further studies.

BackgroundJusticia adhatoda is an important medicinal plant traditionally used in the Indian system of medicine and the absence of molecular-level studies on this plant hinders its wide use, hence the study was aimed to analyse the genes involved in various pathways.Methods and ResultsThe RNA isolated was subjected to Illumina sequencing. De novo assembly was performed using TRINITY software which produced 171.064 transcripts with 55,528 genes and N50 value of 2065bp, followed by annotation of unigenes against NCBI, KEGG and Gene Ontology with 105572 annotated unigenes and 40288 non-annotated unigenes. A total of 5980 unigenes were annotated to 144 biochemical pathways, including the metabolism and biosynthesis pathways. The pathway analysis revealed the major transcripts involved in the tryptophan biosynthesis with TPM values of 6.0903, 33.6854, 11.527, 1.6959, and 8.1662 for Anthranilate synthase alpha, Anthranilate synthase beta, Arogenate/Prephenate dehydratase, Chorismate synthase and Chorismate mutase, respectively. The qRT-PCR validation of the key enzymes showed up-regulation in mid mature leaf when compared to root and young leaf tissue. A total of 16,154 SSRs were identified from the leaf transcriptome of J. adhatoda,which could be helpful in molecular breeding.ConclusionThe study aimed at identifying uni-transcripts involved in the tryptophan biosynthesis pathway for its medicinal properties, as it acts as a precursor to the acridone alkaloid biosynthesis with major key enzymes and their validation. This is the first study that reports transcriptome assembly and annotation of the J. adhatoda plant.