Fig 1.
Workflow for Illumina sequencing, de novo assembly, annotation, and other analysis carried out in the leaf transcriptome of Cassia angustifolia.
Table 1.
Throughput and quality of Illumina sequencing of Cassia angustifolia leaf transcriptome.
Table 2.
Assembly and CDS statistics of Illumina sequencing of Cassia angustifolia in the leaf transcriptome.
Table 3.
Distribution of blast results of CDS in the Cassia. angustifolia leaf transcriptome.
Fig 2.
GO Classification in A) young and B) mature leaf transcriptome of Cassia angustifolia.
Cassia angustifolia 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 C. angustifolia transcripts showed homology to uncharacterised proteins annotated as unknown, hypothetical and expressed proteins.
Fig 3.
Clusters of orthologous groups (COG) functional classification of CDS in the young and mature leaf transcriptome of Cassia angustifolia.
Fig 4.
Distribution of the different classes of Transcription factors in the leaf transcriptome of Cassia angustifolia.
Fig 5.
Top 10 Pfam domains represented in InterProScan transcript annotations of the Cassia angustifolia leaf Transcriptome.
Fig 6.
KEGG pathway analysis of CDS in the young and mature leaf transcriptome of Cassia angustifolia.
Fig 7.
Mapping of the genes expressing differentially in young vs mature leaf on the putative sennoside biosynthetic pathway in Cassia angustifolia.
DAHPS:3-deoxy-7-phosphoheptulonate synthase[EC:2.5.1.54], DHQS: 3-dehydroquinate synthase[EC:4.2.3.4],DHQS/SDH: 3-dehydroquinate dehydratase / shikimate dehydrogenase[EC:4.2.1.10 1.1.1.25], SMK: shikimate kinase[EC:2.7.1.71], EPSP Synthase: 3-phosphoshikimate 1-carboxyvinyltransferase/enolpyruvylshikimate phosphate synthase [EC:2.5.1.19], chorismate synthase [EC:4.2.3.5] menF: isochorismate synthase [EC:5.4.4.2], menF/menD/menH/menC or PHYLLO: isochorismate synthase / 2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate synthase / 2-succinyl-6-hydroxy-2,4-cyclohexadiene-1-carboxylate synthase / O-succinylbenzoate synthase[EC:5.4.4.2 2.2.1.9 4.2.99.20 4.2.1.113], menE: Succinylbenzoic acid-CoA ligase/acyl-activating enzyme 14 [EC:6.2.1.26], menB: naphthoate synthase[EC:4.1.3.36], DXPS: 1-deoxy-D-xylulose-5-phosphate synthase[EC:2.2.1.7], DXR: 1-deoxy-D-xylulose-5-phosphate[EC:1.1.1.267], ISPD: 2-C-methyl-D-erythritol 4-phosphate cytidylyltransferase [EC:2.7.7.60], CDPMEK:4-diphosphocytidyl-2-C-methyl-D-erythritol kinase[EC:2.7.1.148], ISPF: 2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase[EC:4.6.1.12], HDS: (E)-4-hydroxy-3-methylbut-2-enyl-diphosphate synthase[EC:1.17.7.1], HDR: 4-hydroxy-3-methylbut-2-enyl diphosphate reductase[EC:1.17.1.2], ACCP Transferase: acetyl-CoA C-acetyltransferase [EC:2.3.1.9], HMGS:hydroxymethylglutaryl-CoA synthase [EC:2.3.3.10], HMGR: hydroxymethylglutaryl-CoA reductase (NADPH) [EC:1.1.1.34], MK: mevalonate kinase[EC:2.7.1.36], PMK: phosphomevalonate kinase [EC:2.7.4.2], MPD: diphosphomevalonate decarboxylase[EC:4.1.1.33], IPPS: isopentenyl-diphosphate delta-isomerase[EC:5.3.3.2], PKS: Polyketide Synthase, PKC:Polyketide Cyclase, UGT:UDP-Glucosyl Transferase; Y_ID:Young leaf CDS ID number for enzyme, M_ID:Mature leaf CDS ID number for enzyme, Y_FPKM: Young leaf CDS FPKM value, M_FPKM: Mature leaf CDS FPKM value, Log Fold Change: Log of change in folds of expression of CDS in young compared to matured leaf transcripts.
Table 4.
Putative genes involved in sennoside biosynthesis identified in the leaf transcriptome of Cassia angustifolia.
Fig 8.
Heat map of top 100 differentially expressed genes in young and mature leaf transcriptome of Cassia angustifolia.
Fig 9.
FPKM values based gene expression of annotated cytochrome P450s (CYPs) in leaf transctiptome of Cassia angustifolia.
Table 5.
Differential expression of genes involved in the sennoside biosynthesis in the Cassia angustifolia leaf transcriptome.
Table 6.
Statistics of SSRs identified using MISA in the leaf transcriptome of Cassia angustifolia.
Fig 10.
Variation in the total sennoside content (%) with ontogeny of the leaves.