Figure 1.
Plant histone modifiers and their site of modification on the H3 and H4 histone tails.
The figure represents the histone modifications on specific residues of H3 and H4 histone tails with the different histone modifiers. Several of the basic amino acids – Lysine (K), Arginine (R) are targeted for histone acetylation/deacetylation, histone lysine methylation/demethylation and arginine methylation/demethylation by numerous histone modifying enzymes –histone acetyltransferase (HAG, HAF, HAM ), histone deacetylase (HDA), histone methyltransferase (ATX, ATXR, ATHR, SUVH, SUVR, CLF, MEA, SWN, ASHH), Jumonji demethylase (JMJ), Early flowering 6 (ELF6), Relative of ELF6 (REF6), protein arginine methyltransferase (PRMT).
Figure 2.
Soybean shoot apical meristem development from vegetative to reproductive stage.
Micrograph of scanning electron microscopy of soybean shoot apical meristem from plants of 10 days old, after 4 and 10 short-days (SD) respectively. Shoot apical meristem (SAM), Floral meristem (FM). Micrograph were adapted with permission of John Wiley and Sons from[53].
Figure 3.
Phylogenetic tree and domain architecture of histone acetyltransferase (HATs).
Neighbour-Joining phylogenetic tree are constructed based on protein alignments of Arabidopsis and soybean HATs proteins using ClustalX2. Bootstrap values greater than 50% are shown at the nodes and tree is drawn to given scale of branch lengths. The schematic diagrams show the domain organization of these proteins according to analysis by NCBI Batch-CD, SMART and PFAM searches. Different domains are indicated by the use of different colours as shown at the bottom of the figure. The accession numbers for the sequences used in the alignment are listed in the figure.
Figure 4.
Expression profile and evolutional pattern of histone acetyltransferase (HATs).
The heat map shows the relative abundances of soybean genes identified. The highest expression level for each gene across different samples is given in RPKM value. The level of expression for a gene across different samples are represented as percentage of the maximum expression level in colour code from 0% (white) to 100% (black). Heat maps were plotted against the phylogenetic tree constructed using soybean protein sequences and GO annotation. L0, L1, L2, and L3 were leaves at 0 short-day, 1 short-day, 2 short-day, and 3 short-day; S0, S1, S2, S3, and S4 were shoot apical meristems at 0 short-day, 1 short-day, 2 short-day, 3 short-day and 4 short-day.
Figure 5.
Phylogenetic tree and domain architecture of histone deacetylase (HDACs).
Neighbour-Joining phylogenetic tree are constructed based on protein alignments of Arabidopsis and soybean HATs proteins using ClustalX2. Bootstrap values greater than 50% are shown at the nodes and tree is drawn to given scale of branch lengths. The schematic diagrams show the domain organization of these proteins according to analysis by NCBI Batch-CD, SMART and PFAM searches. Different domains are indicated by the use of different colours as shown at the bottom of the figure. The accession numbers for the sequences used in the alignment are listed in the figure.
Figure 6.
Expression profile and evolutional pattern of histone deacetylase (HDACs).
The heat map shows the relative abundances of soybean genes identified. The highest expression level for each gene across different samples is given in RPKM value. The level of expression for a gene across different samples are represented as percentage of the maximum expression level in colour code from 0% (white) to 100% (black). Heat maps were plotted against the phylogenetic tree constructed using soybean protein sequences and GO annotation. L0, L1, L2, and L3 were leaves at 0 short-day, 1 short-day, 2 short-day, and 3 short-day; S0, S1, S2, S3, and S4 were shoot apical meristems at 0 short-day, 1 short-day, 2 short-day, 3 short-day and 4 short-day.
Figure 7.
Phylogenetic tree and domain architecture of histone methyltransferase (HMTs).
Neighbour-Joining phylogenetic tree are constructed based on protein alignments of Arabidopsis and soybean HATs proteins using ClustalX2. Bootstrap values greater than 50% are shown at the nodes and tree is drawn to given scale of branch lengths. The schematic diagrams show the domain organization of these proteins according to analysis by NCBI Batch-CD, SMART and PFAM searches. Different domains are indicated by the use of different colours as shown at the bottom of the figure. The accession numbers for the sequences used in the alignment are listed in the figure.
Figure 8.
Expression profile and evolutional pattern of histone methyltransferase (HMTs).
The heat map shows the relative abundances of soybean genes identified. The highest expression level for each gene across different samples is given in RPKM value. The level of expression for a gene across different samples are represented as percentage of the maximum expression level in colour code from 0% (white) to 100% (black). Heat maps were plotted against the phylogenetic tree constructed using soybean protein sequences and GO annotation. L0, L1, L2, and L3 were leaves at 0 short-day, 1 short-day, 2 short-day, and 3 short-day; S0, S1, S2, S3, and S4 were shoot apical meristems at 0 short-day, 1 short-day, 2 short-day, 3 short-day and 4 short-day.
Figure 9.
Phylogenetic tree and domain architecture of protein arginine methyltransferase (PRMTs).
Neighbour-Joining phylogenetic tree are constructed based on protein alignments of Arabidopsis and soybean HATs proteins using ClustalX2. Bootstrap values greater than 50% are shown at the nodes and tree is drawn to given scale of branch lengths. The schematic diagrams show the domain organization of these proteins according to analysis by NCBI Batch-CD, SMART and PFAM searches. Different domains are indicated by the use of different colours as shown at the bottom of the figure. The accession numbers for the sequences used in the alignment are listed in the figure.
Figure 10.
Expression profile and evolutional pattern of protein arginine methyltransferase (PRMTs).
The heat map shows the relative abundances of soybean genes identified. The highest expression level for each gene across different samples is given in RPKM value. The level of expression for a gene across different samples are represented as percentage of the maximum expression level in colour code from 0% (white) to 100% (black). Heat maps were plotted against the phylogenetic tree constructed using soybean protein sequences and GO annotation. L0, L1, L2, and L3 were leaves at 0 short-day, 1 short-day, 2 short-day, and 3 short-day; S0, S1, S2, S3, and S4 were shoot apical meristems at 0 short-day, 1 short-day, 2 short-day, 3 short-day and 4 short-day.
Figure 11.
Phylogenetic tree and domain architecture of Jumonji proteins (JmjCs).
Neighbour-Joining phylogenetic tree are constructed based on protein alignments of Arabidopsis and soybean HATs proteins using ClustalX2. Bootstrap values greater than 50% are shown at the nodes and tree is drawn to given scale of branch lengths. The schematic diagrams show the domain organization of these proteins according to analysis by NCBI Batch-CD, SMART and PFAM searches. Different domains are indicated by the use of different colours as shown at the bottom of the figure. The accession numbers for the sequences used in the alignment are listed in the figure.
Figure 12.
Expression profile and evolutional pattern of Jumonji proteins (JmjCs).
The heat map shows the relative abundances of soybean genes identified. The highest expression level for each gene across different samples is given in RPKM value. The level of expression for a gene across different samples are represented as percentage of the maximum expression level in colour code from 0% (white) to 100% (black). Heat maps were plotted against the phylogenetic tree constructed using soybean protein sequences and GO annotation. L0, L1, L2, and L3 were leaves at 0 short-day, 1 short-day, 2 short-day, and 3 short-day; S0, S1, S2, S3, and S4 were shoot apical meristems at 0 short-day, 1 short-day, 2 short-day, 3 short-day and 4 short-day.
Figure 13.
Expression cluster analysis of 152 histone modifiers genes in soybean.
The samples included are 152 soybean histone modifiers genes identified in this study and their expression ratio (log2 RPKM) from nine samples during flowering initiation process. K-means clustering was performed with Person correlation algorithm and number of clusters = 10 and number of iterations = 50. The grey line show expression patterns of each gene and the purple line represent the average expression profile of particular cluster (cluster 1 - 10). L0, L1, L2, and L3 were leaves at 0 short-day, 1 short-day, 2 short-day, and 3 short-day; S0, S1, S2, S3, and S4 were shoot apical meristems at 0 short-day, 1 short-day, 2 short-day, 3 short-day and 4 short-day.
Figure 14.
An outline of RNA-mediated chromatin silencing pathway showing soybean homologues for Arabidopsis RNAi genes.
Pol IV (RNA polymerase IV), RDR 2 (RNA-dependent RNA polymerase 2), SGS3 (Suppressor of gene silencing), DCL (Dicer-like), HEN1, DRB (Double-strand RNA binding), AGO4 (Argonaute 4), Pol V (RNA polymerase V), DRM (Domains rearraged DNA methylation 2), CMT3 (Chromomethylae 3), MET1 (Methyltransferase 1), ROS1 (Repressor of silencing), DME (Demeter).
Figure 15.
List of RNAi associated genes identified in soybean and their expression patterns during flowering initiation.
The heat map shows the relative abundances of soybean genes identified. The highest expression level for each gene across different samples is given in RPKM value. The level of expression for a gene across different samples are represented as percentage of the maximum expression level in colour code from 0% (white) to 100% (black). L0, L1, L2, and L3 were leaves at 0 short-day, 1 short-day, 2 short-day, and 3 short-day; S0, S1, S2, S3, and S4 were shoot apical meristems at 0 short-day, 1 short-day, 2 short-day, 3 short-day and 4 short-day.
Figure 16.
Phylogenetic tree of Argonaute proteins (AGO).
Neighbour-Joining phylogenetic tree are constructed based on protein alignments of Arabidopsis and soybean HATs proteins using ClustalX2. Bootstrap values greater than 50% are shown at the nodes and tree is drawn to given scale of branch lengths. Heat maps were plotted against the phylogenetic tree constructed using soybean protein sequences and GO annotation. L0, L1, L2, and L3 were leaves at 0 short-day, 1 short-day, 2 short-day, and 3 short-day; S0, S1, S2, S3, and S4 were shoot apical meristems at 0 short-day, 1 short-day, 2 short-day, 3 short-day and 4 short-day.