Towards developing a genetic linkage map of isabgol (Plantago ovata Forsk.), a medicinal plant with potent laxative properties

Genetic linkage maps facilitate the genetic dissection of complex traits and comparative analyses of genome structure, as well as molecular breeding in species of economic importance. Isabgol [Plantago ovata (Forsk.)], a medicinal plant with potent laxative properties is used in several tradi-tional systems of Medicines and cultivated in India. We explored the DNA sequences of Isabgol in the Genbank (NCBI) and developed over 1500 simple sequence repeats (SSR) markers. Some of them were validated through DNA amplification. Transferability of SSRs from wild Plantago species viz., P. major, P. coronopus, P. lancelolata, P. maritina and P. intermida into Plantago ovata was stud-ied. We developed a genetic linkage map using recombinant inbred lines (RILs) population which comprises of 30 random amplified polymorphic DNA (RAPD) markers spreading across 11 linkage groups (PO-1 to PO-11) with a total map distance of 75.6 cM. The SSR markers developed will have applications in assessing the functional diversity, comparative mapping and other applications in isabgol

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Not AvailableGymnema sylvestre is an important medicinal plant containing antidiabetic activity. Through de novo transcriptomic study, the pathways of polyoxypregnane glycosides were explored and candidate genes of these pathways were identified in G. sylvestre. High-quality raw reads were assembled into transcripts which resulted in 193,615 unigenes. These unigenes further decoded 58,274 coding DNA sequences (CDSs). Functional annotation of predicted CDSs was carried out using the protein databases, i.e., NCBI’s non-redundant, Uniprot and Pfam. Eukaryotic orthologous group (KOG) classification and transcription factor analysis has revealed most CDS-enriched categories as “Signal transduction mechanism” and “Basic Helix loop helix” (bHLH) transcription factor family, respectively. A total of 16,569 CDSs were assigned minimum one Gene Ontology (GO) term. Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis disclosed 235 CDSs which represented total 27 genes of pregnane glycoside pathways and 19 CDSs represented 10 important enzymes of polyoxypregnane glycoside biosynthesis, i.e., sterol 24-C-methyltransferase, cycloeucalenol cycloisomerase, Δ14-sterol reductase, C-8,7 sterol isomerase, sterol methyltransferase 2, C-5 sterol desaturase, sterol Δ7 reductase, Δ24 sterol reductase, 3β-hydroxysteroid dehydrogenase and progesterone 5β reductase (5βPOR). This transcriptome analysis provided an important resource for future functional genomic studies in G. sylvestre.GSBTM, GUJARA

De novo transcriptome analysis deciphered polyoxypregnane glycoside biosynthesis pathway in Gymnema sylvestre

Gymnema sylvestre is an important medicinal plant containing antidiabetic activity. Through de novo transcriptomic study,the pathways of polyoxypregnane glycosides were explored and candidate genes of these pathways were identified in G.sylvestre. High-quality raw reads were assembled into transcripts which resulted in 193,615 unigenes. These unigenes furtherdecoded 58,274 coding DNA sequences (CDSs). Functional annotation of predicted CDSs was carried out using the proteindatabases, i.e., NCBI’s non-redundant, Uniprot and Pfam. Eukaryotic orthologous group (KOG) classification and transcriptionfactor analysis has revealed most CDS-enriched categories as “Signal transduction mechanism” and “Basic Helix loophelix” (bHLH) transcription factor family, respectively. A total of 16,569 CDSs were assigned minimum one Gene Ontology(GO) term. Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis disclosed 235 CDSs which representedtotal 27 genes of pregnane glycoside pathways and 19 CDSs represented 10 important enzymes of polyoxypregnane glycosidebiosynthesis, i.e., sterol 24-C-methyltransferase, cycloeucalenol cycloisomerase, Δ14-sterol reductase, C-8,7 sterol isomerase,sterol methyltransferase 2, C-5 sterol desaturase, sterol Δ7 reductase, Δ24 sterol reductase, 3β-hydroxysteroid dehydrogenaseand progesterone 5β reductase (5βPOR). This transcriptome analysis provided an important resource for future functionalgenomic studies in G. sylvestre

Deep sequencing-based de novo transcriptome analysis reveals biosynthesis of gymnemic acid in Gymnema sylvestre (Retz.) Schult

Not AvailableGymnema sylvestre extract is used to cure the diabetes mellitus which is an important life style disease. Triterpene saponins having anti-diabetic property from G. sylvestre leaves belonging to oleanane and dammarene classes are collectively known as gymnemic acid. Genomic resources focused on biosynthesis of these molecules are not available. De novo transcriptome sequencing of leaf, flower and fruits of G. sylvestre genotype DGS-22 produced 60.95, 56.99 and 45.82 million raw reads. Quality raw reads were assembled into 112583, 203145 and 138343 set of unigenes for leaf, flower and fruit, respectively from which coding DNA sequences (CDSs) were predicted. Total of 71676, 99643 and 92770 CDSs were annotated against protein databases for leaf, flower and fruit, respectively. The Blast2GO was used to compare and determine the GO annotations. A total of 22933, 30420,29631 and 33282 CDSs of leaf, flower, fruit and master assembly, respectively were assigned at least one GO term. Pathway mapping based on master assembly using KEGG database revealed probable candidate genesinvolved in gymnemic acid biosynthesis which showed that there were total of 287 CDSs encoding genes involved in the gymnemic acid pathway. Validation and expression profiling of nine genes through real time PCR showed up regulation of these genes in leaves of DGS 22 as compared to DGS 3 confirming efficient gymnemicacid biosynthesis in DGS 22 which was in accordance with chemo-profiling of these genotypes. Based on theavailable information from the master assembly, a putative pathway of the gymnemic acid biosynthesis isproposed.Not Availabl

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Not AvailableAshwagandha (W. somnifera Dunal. Linn.), known as Indian ginseng, contains three major bioactive compounds, withaferin-A (WA), 12-deoxywithastramonolide (WO) and withanoloide A (WD). In a field experiment, the impacts of foliar application of growth retardants/promoters was assessed with respect to biomass allocation pattern and major withanoloide content at different phenological stages in W. somnifera. Biomass accumulation pattern showed that foliar application of 500 mg l 1 ethrel at 50, 65, 85, 105, and 120 days after sowing (DAS) restricted phenological progression and reduced berry weight by 61% as comparted to the control at 160 DAS. 500 mg l 1 succinic acid foliar application resulted in maximum plant height (56.4 cm), maximum dry stem weight (DWS) and dry root weight (DRW) whereas 500 mg l 1 ethrel had resulted in minimum plant height and DRW at 180 DAS. During last 50 days of crop growth, the accumulation pattern drastically changed with more than 60% of the biomass allotment to the reproductive part, the berries. The WD in roots ranged between 0.325 mg g 1 and 0.342 mg g 1 during all growth stages. WA content decreased with increase in progression of crop growth and reached the lowest at 180–190 DAS. In a pot experiment, ethrel application up regulated DWF-5 by 2.44, SQE by 3.79 and CYP450s by 1.17 log2fold in roots 8 h after treatment and succinic acid had up regulated the expression of all these genes by nearly 3 log2fold change. This is in accordance with the withanoloide accumulation pattern in field condition under foliar application of these molecules.Not Availabl

Next Generation Sequencing and Transcriptome Analysis Predicts Biosynthetic Pathway of Sennosides from Senna (<i>Cassia angustifolia</i> Vahl.), a Non-Model Plant with Potent Laxative Properties

<div><p>Senna (<i>Cassia angustifolia</i> Vahl.) is a world’s natural laxative medicinal plant. Laxative properties are due to sennosides (anthraquinone glycosides) natural products. However, little genetic information is available for this species, especially concerning the biosynthetic pathways of sennosides. We present here the transcriptome sequencing of young and mature leaf tissue of <i>Cassia angustifolia</i> using Illumina MiSeq platform that resulted in a total of 6.34 Gb of raw nucleotide sequence. The sequence assembly resulted in 42230 and 37174 transcripts with an average length of 1119 bp and 1467 bp for young and mature leaf, respectively. The transcripts were annotated using NCBI BLAST with ‘green plant database (txid 33090)’, Swiss Prot, Kyoto Encylcopedia of Genes & Genomes (KEGG), Cluster of Orthologous Gene (COG) and Gene Ontology (GO). Out of the total transcripts, 40138 (95.0%) and 36349 (97.7%) from young and mature leaf, respectively, were annotated by BLASTX against green plant database of NCBI. We used InterProscan to see protein similarity at domain level, a total of 34031 (young leaf) and 32077 (mature leaf) transcripts were annotated against the Pfam domains. All transcripts from young and mature leaf were assigned to 191 KEGG pathways. There were 166 and 159 CDS, respectively, from young and mature leaf involved in metabolism of terpenoids and polyketides. Many CDS encoding enzymes leading to biosynthesis of sennosides were identified. A total of 10,763 CDS differentially expressing in both young and mature leaf libraries of which 2,343 (21.7%) CDS were up-regulated in young compared to mature leaf. Several differentially expressed genes found functionally associated with sennoside biosynthesis. CDS encoding for many CYPs and TF families were identified having probable roles in metabolism of primary as well as secondary metabolites. We developed SSR markers for molecular breeding of senna. We have identified a set of putative genes involved in various secondary metabolite pathways, especially those related to the synthesis of sennosides which will serve as an important platform for public information about gene expression, genomics, and functional genomics in senna.</p></div

Workflow for Illumina sequencing, de novo assembly, annotation, and other analysis carried out in the leaf transcriptome of <i>Cassia angustifolia</i>.

<p>Workflow for Illumina sequencing, de novo assembly, annotation, and other analysis carried out in the leaf transcriptome of <i>Cassia angustifolia</i>.</p

Assembly and CDS statistics of Illumina sequencing of <i>Cassia angustifolia</i> in the leaf transcriptome.

<p>Assembly and CDS statistics of Illumina sequencing of <i>Cassia angustifolia</i> in the leaf transcriptome.</p

GO Classification in A) young and B) mature leaf transcriptome of <i>Cassia angustifolia</i>.

<p><i>Cassia angustifolia</i> CDS were searched against the non-redundent protein sequences available in the Uni-ProtKB/SwisProt database using BLASTX with E value threshold of 1e^-06 in order to assign putative function. Out of 42,230 and 37,174 CDS in young and mature leaf respectively, 29,944 (70.9%) CDS in young and 28,099 (75.5%) CDS in mature leaf transcriptome showed significant hits to the Uni-ProtKB/SwisProt data set thereby showing overall gene conservation. In addition, many <i>C</i>. <i>angustifolia</i> transcripts showed homology to uncharacterised proteins annotated as unknown, hypothetical and expressed proteins.</p