Fig 1.
Tissues of N. cadamba used in deep sequencing.
(A) The whole plant of greenhouse-grown N. cadamba. (B) The apical, middle and basal stem segments with bark from N. cadamba. (C) Phloroglucinol staining of transverse stem section. (D) Magnified view of red box region in C. Scale bar: A = 10 cm, B = 1 cm, C = 1 mm and D = 200 μm.
Table 1.
RNA-Seq data summary for all samples.
Table 2.
Length distribution of assembled contigs, transcripts, UniGenes and predicted ORFs of UniGenes.
Table 3.
Summary for UniGene functional annotation.
Fig 2.
Characteristics of the homology search of N. cadamba UniGenes in the nr database.
(A) E-value distribution of the top BLASTx hits against the nr database for each UniGene. (B) Number and percentage of UniGenes matching the 17 top species using BLASTx in the nr database.
Fig 3.
DEGs Venn diagram and expression profile.
(A) Venn diagram of DEGs. A, apical stem segment; M, middle stem segment; B, basal stem segment. (B) Four expression profiles of DEGs. I and IV indicate UniGenes which are up-regulated and down-regulated, respectively, and II and III indicate those with irregular expression. Twenty-five UniGenes were selected for the diagram for each expression profile.
Fig 4.
N. cadamba UniGenes in the transcriptional network regulating secondary cell wall (SCW) biosynthesis according to A. thaliana.
Light grey boxes indicate major transcription factors of the Arabidopsis transcriptional network leading to biosynthesis of the three major SCW constituents. Light blue boxes indicate N. cadamba putative UniGenes encoding orthologues. * indicates the DEGs. Yellow-blue scale and white-red scale indicate relative and absolute expression profiles, respectively. A, apical stem segment; M, middle stem segment; B, basal stem segment. Absolute expression level (RPKM) is only shown for the basal stem segment.
Fig 5.
UniGenes involved in cellulose and mannan biosynthesis in wood-forming tissues of N. cadamba.
Sugar and polymer intermediates are shown in black, whereas the proteins (enzymes) involved in each step are shown in blue. Detailed protein names, annotation and RNA-Seq expression data are provided in S12 File. * indicates the DEGs. Yellow-blue scale and white-red scale indicate relative and absolute expression profiles, respectively. A, apical stem segment; M, middle stem segment; B, basal stem segment. Absolute expression level (RPKM) is only shown for basal stem segment. CESA, cellulose synthase; CSLA, cellulose synthase like A; FRK, fructokinase; GMP, GDP-D-mannose pyrophosphorylase; HEX, hexokinase; INV, invertase; PGI, phosphoglucose isomerase; PGM, phosphoglucomutase; PMI, phosphomannose isomerase; PMM, phosphomannomutase; SUSY, sucrose synthase; UGP, UDP-glucosepyrophosphorylase.
Table 4.
Comparison in number of genes that encode eleven key enzymes in the monolignol biosynthesis pathway among A. thaliana, N. cadamba, P. trichocarpa and E. grandis.
Fig 6.
UniGenes involved in lignin biosynthesis in wood forming tissues of N. cadamba.
Phenylalanine, intermediates and monolignols are shown in black, while the proteins (enzymes) involved in each step are shown in blue. Detailed protein names, annotation and RNA-Seq expression data are provided in S13 File. * indicates the DEGs. Yellow-blue scale and white-red scale indicate relative and absolute expression profiles, respectively. A, apical stem segment; M, middle stem segment; B, basal stem segment. Absolute expression level (RPKM) is only shown for basal stem segment. 4CL, 4-coumarate: CoA ligase; C3H, p-coumarate 3-hydroxylase; C4H, cinnamate 4-hydroxylase; CAD, cinnamyl alcohol dehydrogenase; CCoAOMT, caffeoyl-CoA O-methyltransferase; CCR, cinnamoyl-CoA reductase; COMT, caffeic acid O-methyltransferase; CSE, Caffeoylshikimate esterase; F5H, ferulate 5-hydroxylase; HCT, p-hydroxycinnamoyl-CoA: quinate shikimate p-hydroxycinnamoyltransferase; PAL, phenylalanine ammonia-lyase.
Fig 7.
UniGenes involved incadambine, triterpenoid saponin and phytosterol biosynthesis.
Intermediates, cadambine, triterpenoid saponins and phytosterols are shown in black, whereas the proteins (enzymes) involved in each step are shown in blue. Detailed protein names, annotation and RNA-Seq expression data are provided in S15 File. * indicates the DEGs. Yellow-blue scale and white-red scale indicate relative and absolute expression profiles, respectively. A, apical stem segment; M, middle stem segment; B, basal stem segment. Absolute expression level (RPKM) is only shown for basal stem segment. CAS, Cycloartenol cyclase; FPS, farnesyl diphosphate synthase; G10H, geraniol 10-hydroxylase; GES, geraniol synthase; GPPS, geranyl diphosphate synthase; SLS, secologanin synthase; SQE, squalene epoxidase; SQS, Squalene synthase; STR, strictosidinesynthase; TDC, tryptophan decarboxylase; TS, tryptophan synthase; β-AS, β-amyrin synthase.
Fig 8.
Expression of UniGenes related to transcription factors regulating SCW biosynthesis, lignin, or cellulose biosynthesis.
Error bars on each column indicate SEs from three replicates. A, apical stem segment; M, middle stem segment; B, basal stem segment.