Table 1.
Length distribution of contigs, scaffolds and unigenes.
Fig 1.
The distribution of the number of reads based on the relative position in gene (5′-3′).
Fig 2.
The dependence of unigene lengths on the number of reads assembled into each unigene.
Table 2.
Functional annotation of the D. sinicus transcriptome.
Fig 3.
Species distribution of the BLAST hits in Nr dababase.
56,587 BLASTX-hit unigenes were calculated.
Fig 4.
Functional annotation of assembled sequences based on gene ontology (GO) categorization.
The unigenes are summarized into three main categories: cellular component, molecular function and biological process.
Fig 5.
Clusters of orthologous groups (COG) classification.
In total, 21,009 of the 81,744 sequences with Nr hits were grouped into 25 classifications.
Table 3.
Frequency of SSRs.
Fig 6.
The distribution of SSR motif length.
Table 4.
Statistics of SNP types.
Table 5.
Number of genes found in the bamboos and rice genome that encode key enzymes involved in the lignin biosynthesis pathway.
Fig 7.
The diagram of metabolic pathway involved in lignin biosynthesis.
It was completed according to Baucher et al. (1998) [71]. All metabolic enzymes predicted in D. sinicus transcriptome were marked with red font. 4CL: 4-coumarate CoA ligase; C3H: Coumarate 3-hdroxylase; C3′H: Coumaroylquinate (coumaroylshikimate) 3′-monooxygenase; C4H: Cinnamate 4-hydroxylase; CAD: Cinnamyl alcohol dehydrogenase; CCoAOMT: Caffeoyl-CoA 3-O-methyltransferase; CCR: Cinnamoyl-CoA reductase; COMT: Caffeic acid 3-O-methyltransferase; F5H: Ferulate 5-hydroxylase; HCT: Hydroxycinnamoyl-CoA: shikimate/quinate hydroxycinnamoyltransferase; PAL: Phenylalanine ammonia lyase; PTAL: Phenylalanine/tyrosine ammonia-lyase; PER: Peroxidase.
Fig 8.
Phylogenic analysis of Shikimate O-hydroxycinnamoyltransferase.
Two clades (A and B) that represent different likely enzymatic function of 27 D. sinicus unigenes were pointed. In the Fig, unigene number was denoted using underline. Besides D. sinicus transcriptome data, other protein sequences encoding Shikimate O-hydroxycinnamoyltransferase were obtained from NCBI. To distinctly display the relationship between D. sinicus and other species, the species name of each sequence was marked out, and the corresponding accession numbers were as follows: Amborella trichopoda, XP_011620549.1; Brassica napus, XP_013719902.1; Camelina sativa, XP_010478899.1; Cucumis melo, XP_008466864.1; C. sativus, NP_001295843.1; Glycine max, XP_003543709.1; Gossypium raimondii, XP_012445417.1; Elaeis guineensis, XP_010942061.1; Fragaria vescasubsp.vesca, XP_011467012.1; Jatropha curcas, XP_012071524.1; Malus domestica, XP_008380698.1; Nelumbo nucifera, XP_010256176.1; Nicotiana sylvestris, XP_009789449.1; Phaseolus vulgaris, AGV54440.1; Phoenix dactylifera, XP_008790160.1; Populus euphratica, XP_011031277.1; P. trichocarpa, XP_006368492.1; Pyrus × bretschneideri, XP_009344995.1; Sesamum indicum, XP_011073311.1; Solanum tuberosum, XP_006343633.1; S. lycopersicum, XP_004235891.1; Tarenaya hassleriana, XP_010545447.1; Trifolium pretense, ACI16630.1; Vitis vinifera, XP_002268988.1; Zea mays, XP_008673748.1.
Table 6.
The most abundant transcription factors found in D. sinicus transcriptome.
Fig 9.
Unigenes of D. sinicus involved in photosynthesis (A) and antenna protein (B).
The pathways are originated from KEGG. The enzymes detected in D. sinicus transcriptome were marked with red frame in the pathway. 1.18.1.2: Ferredoxin-NADP+ reductase; 1.10.9.1: cytochrome b6-f complex iron-sulfur subunit; 3.6.3.14: F-type H+-transporting ATPase subunit a; PsbA: photosystem II P680 reaction center D1 protein; PsbC: photosystem II CP43 chlorophyll apoprotein; PsbB: photosystem II CP47 chlorophyll apoprotein; PsbK: photosystem II PsbK protein; PsbM: photosystem II PsbM protein; PsbH: photosystem II PsbH protein; PsbI: photosystem II PsbI protein; PsbO: photosystem II oxygen-evolving enhancer protein 1; PsbP: photosystem II oxygen-evolving enhancer protein 2; PsbQ: photosystem II oxygen-evolving enhancer protein 3; PsbR: photosystem II 10kDa protein; PsbS: photosystem II 22kDa protein; PsbT: photosystem II PsbT protein; PsbW: photosystem II PsbW protein; PsbY: photosystem II PsbY protein; PsbZ: photosystem II PsbZ protein; Psb28: photosystem II 13kDa protein; PsaA: photosystem I P700 chlorophyll a apoprotein A1; PsaB: photosystem I P700 chlorophyll a apoprotein A2; PsaC: photosystem I subunit VII; PsaD: photosystem I subunit II; PsaE: photosystem I subunit IV; PsaF: photosystem I subunit III; PsaG: photosystem I subunit V; PsaH: photosystem I subunit VI; PsaI: photosystem I subunit VIII; PsaK: photosystem I subunit X; PsaL: photosystem I subunit XI; PsaN: photosystem I subunit PsaN; PsaO: photosystem I subunit PsaO; PetB: cytochrome b6; PetD: cytochrome b6-f complex subunit 4; PetA: apocytochrome f; PetC: cytochrome b6-f complex iron-sulfur subunit; PetE: plastocyanin; PetF: ferredoxin; PetH: ferredoxin—NADP+ reductase; beta: F-type H+-transporting ATPase subunit beta; alpha: F-type H+-transporting ATPase subunit alpha; gamma: F-type H+-transporting ATPase subunit gamma; delta: F-type H+-transporting ATPase subunit delta; b: F-type H+-transporting ATPase subunit b; Lhca: light-harvesting complex I chlorophyll a/b binding protein; Lhcb: light-harvesting complex II chlorophyll a/b binding protein.
Fig 10.
RT-qPCR validations of 14 genes involved in photosynthesis and lignin synthesis pathways.
Different letters indicate differences at P ≤ 0.05 based on the LSD (least significant difference) test. Data are means of three replicates and each replicate was measured three times. The gene names and the primers used for RT-qPCR analysis are shown in Table 7. AtpC: F-type H+-transporting ATPase subunit c; CAD: Cinnamoyl alcohol dehydrogenase; COMT: Caffeic acid-3-O-methyltransferase; HCT: Shikimate O-hydroxycinnamoyltransferase; PsbA: photosystem II P680 reaction center D1 protein; PsaB: photosystem I P700 chlorophyll a apoprotein A2; PetB: cytochrome b6; PetF: ferredoxin; Lhca2: light-harvesting complex I chlorophyll a/b binding protein 2; Lhca3: light-harvesting complex I chlorophyll a/b binding protein 3; Lhca6: light-harvesting complex I chlorophyll a/b binding protein 6; F5H: ferulate-5-hydroxylase; 4CL: 4-coumarate-CoA ligase.
Table 7.
Quantitative PCR validation of the RNA-seq.