De Novo Transcriptome Analysis of Medicinally Important Plantago ovata Using RNA-Seq

Abstract

Plantago ovata is an economically and medicinally important plant of the family Plantaginaceae. It is used extensively for the production of seed husk for its application in pharmaceutical, food and cosmetic industries. In the present study, the transcriptome of P. ovata ovary was sequenced using Illumina Genome Analyzer platform to characterize the mucilage biosynthesis pathway in the plant. De novo assembly was carried out using Oases followed by velvet. A total of 46,955 non-redundant transcripts (≥100 bp) using ~29 million high-quality paired end reads were generated. Functional categorization of these transcripts revealed the presence of several genes involved in various biological processes like metabolic pathways, mucilage biosynthesis, biosynthesis of secondary metabolites and antioxidants. In addition, simple sequence-repeat motifs, non-coding RNAs and transcription factors were also identified. Expression profiling of some genes involved in mucilage biosynthetic pathway was performed in different tissues of P. ovata using Real time PCR analysis. The study has resulted in a valuable resource for further studies on gene expression, genomics and functional genomics in P. ovata.

Comparative Transcriptome Analysis Uncovers Genes and Pathways Relating to Downy Mildew Resistance in Isabgol (Plantago ovata Forsk.)

“…Higher the N 50 better will be the quality of the assembly. The N50 value found in this study was higher than the previous reports in Isabgol [34],…”

“…We obtained 9.738 GB of raw sequence data which is consistent with the characteristic throughput of Illumina Hi-seq. In general, clean and high-quality reads are essential for good assembly and gene expression analysis [34][35][36][37][38][39][40][41][42][43][44][45], and hence pre-processing was performed to remove low complexity, low length, duplicate, and rRNA reads and de novo assembled into contigs and further to transcripts and CDS. Trinity assembler was used in the present study.…”

“…With respect to Isabgol, only a few studies are on the transcriptomic resources: [34] characterized the mucilage biosynthesis pathways in P. ovata using 46,955 unique transcripts, [35] characterized genes involved in xylan biosynthesis using 1,099158 ESTs and [36] generated 250 Mb whole genome sequence to develop simple sequence repeat (SSR) markers for breeding applications. [37][38] sequenced 5,900 ESTs and 3,247 independent mRNAs from the leaf vascular tissue of Plantago major, a relative of Plantago ovata and no complete transcriptome analysis is available in the public domain to understand DM resistance in Isabgol.…”

Enrichment of genomic resources and identification of simple sequence repeats from medicinally important Clausena excavata

“…In addition, it was lower than the number of genes identified from RNA-seq analysis of other medicinal plants such as Plantago ovata and Isatis indigotica. In Plantago ovata, a total of 46,955 unigenes were identified, of which 28,160 genes were annotated (Kotwal et al 2016). In Isatis indigotica, a total of 33,238 unigenes were assembled, of which 28,184 unigenes were annotated (Tang et al 2014).…”

The complete chloroplast genome sequence of Plantago ovata

“…It is used extensively for the health and production of seed and husk for its application in pharmaceutical and food. In the pharmaceutical field, Plantago ovata has been used to treat cholesterol lowering, diuretic and others, it also has been incorporated into breakfast cereals, instant beverages, bakery and other dietary products in the food field (Kotwal et al 2016). At present, there are few studies on the genome and transcriptome of P. ovata.…”