Fig 1.
The length distribution of transcripts in S. tora.
X and Y axis represent unigene lengths and percent of unigene length distribution, respectively.
Table 1.
Assembly statistics of the S. tora transcriptome by RNA-Seq and Iso-Seq.
Fig 2.
Histogram of gene ontology (GO) classification from RNA-Seq and Iso-Seq.
The results are summarized in three main categories: biological process, molecular function, and cellular component.
Fig 3.
Heat map of top 50 differentially expressed genes between early- and late-stages of seed development in S. tora.
Heatmap showing differentially expressed genes between early and late stages of seed development in S. tora. Color scale representing normalized expression values is shown at the bottom.
Fig 4.
Real-time PCR validation of gene expression obtained via RNA-Seq.
All the real-time PCR experiments were performed at least three times in each independent biological experiment (3 replicates). Error bars represent SEM from triplicates.
Fig 5.
MapMan metabolism overview maps showing differences in transcript levels during seed development.
MapMan software was used to provide a snapshot of modulated genes over the main metabolic pathways. Log2 fold changes values are represented. Up-regulated and down-regulated transcripts are shown in red and blue, respectively.
Fig 6.
LC-MS analysis of anthraquinone during seed development.
Seven anthraquinone levels in the early seed (A) and in the late seed (B).
Table 2.
Anthraquinone contents in the early and late seeds.
Fig 7.
The up-down of putative genes of anthraquinone-biosynthetic pathway in S. tora.
It was normalized to the FPKM to compare the changes in gene expression levels between different parts of S. tora. Total gene expression levels were clustered based on the Log2 (FPKM +1). DXPS, 1-Deoxy-D-xylulose-5-phosphate synthase (EC 2.2.1.7); DXR, 1-Deoxy-D-xylulose-5-phosphate reductoisomerase (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); ACCA, Acetyl-CoA carboxylase (EC 6.4.1.2); HMGS, Hydroxymethylglutaryl-CoA synthase (EC 2.3.3.10); HMGR, Hydroxymethylglutaryl-CoA reductase (EC 1.1.1.34); MK, Mevalonate kinase (EC 2.7.1.36); PMK, Phosphomevalonate kinase (EC 2.7.4.2); MPD, Methyl parathion hydrolase (EC 3.1.8.1); IPPS, Isopentenyl-diphosphate delta-isomerase (EC 5.3.3.2); DAHPS, 3-Deoxy-7-phosphoheptulonate synthase (EC 2.5.1.54); DHQS, 3-Dehydroquinate synthase (EC 4.2.3.4); DHQD/SDH, 3-Dehydroquinate dehydratase/shikimate dehydrogenase (EC 4.2.1.10/1.1.1.25); SMK, Shikimate kinase (EC 2.7.1.71); EPSP, 3-Phosphoshikimate 1-carboxyvinyltransferase (EC 2.5.1.19); CS, Chorismate synthase (EC 4.2.3.5); ICS, Isochorismate synthase (EC 5.4.4.2); PHYLLO, 2-Succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylic acid synthase (EC 2.2.1.9); MenE, 2-Succinylbenzoate-CoA ligase (EC 6.2.1.26); MenB, 1,4-Dihydroxy-2-naphthoyl-CoA synthase (EC 4.1.3.36); GGPS, Geranylgeranyl diphosphate synthase (EC 2.5.1.1); PSY, Phytoene synthase (EC 2.5.1.32); PDS, Phytoene desaturase (EC 1.3.99.30); ZDS, Zeta-carotene desaturase (EC 1.3.5.6); LYCB, Lycopene beta-cyclase (EC 5.5.1.19); LYCE, Lycopene epsilon-cyclase (EC 5.5.1.18); BCH, Beta-carotene hydroxylase (EC 1.14.13.129); ZEP, Zeaxanthin epoxidase (EC 1.14.15.21); PAL, Phenylalanine ammonia-lyase (EC 4.3.1.24); C4H, Cinnamate-4-hydroxylase (EC 1.14.13.11); 4CL, 4-Coumarate-CoA ligase (EC 6.2.1.12); and CHS, Chalcone synthase (EC 2.3.1.74).