Table 1.
Physiochemical properties and secondary structural properties of PeD-Js genes.
Fig 1.
Chromosome location and collinearity analysis of PeD-J genes.
A, Genomic distribution of the PeD-J, PeDIR and PeJRL genes on bamboo chromosomes. The PeD-J genes are numbered 1–4, PeDIR genes are numbered 1–38 and PeJRL genes are numbered 1–19. The scale represents the number of DNA bases. The chromosome number is shown on the left side of each strip, the gene name is on the right side of the chromosome and the purple rectangles represent PeD-J gene family members. B, Gene duplication among PeD-Js, PeDIRs and PeJRLs of bamboo. Green gene names represent the DIR gene family, blue gene names represent the JRL gene family and violet gene names represent the D-J gene family.
Fig 2.
The phylogenetic tree of intraspecific and interspecies relationships.
Phylogenetic trees without roots were constructed using the NJ method in MEGA 7.0. Bootstrap values from 1,000 replicates were indicated at each node. A, The phylogenetic relationships of bamboo (yellow squares), rice (lightblue diamonds), wheat (green squares), barley (darkblue circles) and maize (purple triangles) D-J sequences. Clustering resulted in a tree that is divided into four subfamilies: HvD-Js represent the D-J sequences of barley, OsD-Js represent the D-J sequences of rice, PeD-Js represent the D-J sequences of bamboo and TaD-Js represent the D-J sequences of wheat. B, The inter-species phylogenetic tree of bamboo is divided into three subfamilies, including DIR (black circles), JRL (darkpurple squares) and D-J (blue triangles).
Fig 3.
Genetic structures, conserved domains and multiple sequence alignment.
A, Gene structure. The scale in Figure A represents the length of the nucleotide sequence. UTR, CDS and introns are represented by different colored regions. B, Conserved domains and motifs. The gray bar represents protein sequence length, the number represents the amino acid position. The dirigent domain is composed of the pink region, motif 1 and motif 2, and the jacalin structural domain is composed of the purple region, motif 3 and motif 4. the green region represents motif1, the yellow region represents motif2, the violet region represents motif3 and the lavender region represents motif4. C, Multiple sequence alignment of the PeD-J protein sequences. The number over the sequence indicates the position of the amino acids in the D-J proteins, in this figure. The main motifs that form each domain are outlined in horizontal lines, the motif site is shown below the alignment and the amino acid composition is shown above the alignment. The names of protein sequences are shown on the left side and the amino acids marked in blue represent the binding sites of sugars.
Fig 4.
Protein structures based on homologous modeling.
Protein structures are predicted based on sequence homology to known structures. The region of the substrate-binding is marked. The yellow chain represents the conserved amino acid residues of the dirigent domain region. The red chain represents the conserved amino acid residues involved in β-prismatic folding of the jacalin domain region and the orange chain represents the attached substrates in the substrate-binding center. A, PeD-J01 with jacalin-dirigent domain (blue and purple, PDB: 5GVY), which binds to MAN. B, PeD-J04 with a jacalin-dirigent domain (blue and purple, PDB: 5XFH), which binds to NAG, MAN, BMA or GAL. C, PeD-J03 with a jacalin-dirigent domain (blue and purple, PDB: 5GVY), which binds to MAN. D, PeD-J04 with a jacalin-dirigent domain (blue and purple, PDB: 5XFH), which binds to NAG, MAN, BMA or GAL.
Fig 5.
Promoter cis-element analysis of PeD-J genes.
Promoter cis-element analysis of PeD-Js. The 1500 bp DNA fragments upstream of the ATG are analyzed using the online analysis software PlantCARE. Different cis-acting elements of D-J genes are displayed. A, Promoter position information. The different colored markers indicate different predicted cis-acting elements. B, Promoter number analysis. The color scale to the right of the heat map represents the number of promoters.
Fig 6.
The expression profiles of PeD-J genes.
A, Expression profile of PeD-J genes after GA treatment. B, Expression profile of PeD-J genes after NAA treatment. C, Expression profile of PeD-J genes in the shoots of bamboo at different growth heights. D, Expression profile of PeD-J genes in different tissues. CK represents the control group. Each group has three replicates. The relative expression levels are depicted according to the color scale, where a change from blue to red indicates transcript abundance from low to high. Gene expression is calculated as the sum of the abundance of all transcripts produced by a given gene.
Fig 7.
Expression patterns of PeD-J genes.
The relative expression patterns of PeD-J genes are normalized as transcripts per million (TPM) and expressed as log values. A, Expression pattern after GA treatment. B, Expression pattern after NAA treatment. C, Expression pattern in different tissues. D, Expression pattern in shoots at different growth heights.
Fig 8.
qRT-PCR analyses of PeD-J genes.
A, Expression of PeD-Js in different tissues. B, Expression of PeD-Js in roots under abiotic stress treatment. C, Expression of PeD-Js in stems under abiotic stress treatment. D, Expression of PeD-Js in leaves under abiotic stress treatment. E, Expression of PeD-Js in leaves after MeJA treatment. 20% PEG solution was used to simulate drought. The concentration of salt and MeJA was 200 mM and 100 μM, respectively. Single asterisk indicates that the level of the gene expression in treatment group was significantly different from that in the control group (t-test, p < 0.05). Double asterisks indicate that there is a significant difference (t-test, p < 0.01). The relative expression levels of the target genes were examined using the 2-ΔΔCt method. Error bars represent standard deviations of the means of three independent replicates.
Fig 9.
Subcellular localization analyses of 35S::GFP and 35S:: PeD-J03-GFP.
A, Subcellular localization of 35S::GFP in tobacco leaves. B, Subcellular localization of 35S:: PeD-J03-GFP in tobacco leaves.