Fig 1.
A graphical abstract of our study.
Table 1.
Basic information of M. acuminata DCL, AGO and RDR gene families.
Fig 2.
The multiple sequence alignment analysis of RNase III domains (RIBOc I and II) of the aa sequences of M. acuminata and Arabidopsis DCL proteins by Clustal-W program in MEGA 11.
The downward red arrows indicate the position of conserved The two RNase III domains at the glutamate (E), aspartate (D), glutamate (D), aspartate (E) (EDDE) position.
Fig 3.
PIWI domain of the aa sequences of M. acuminata and Arabidopsis AGO proteins by Clustal-W program in MEGA 11.
The downward red arrows indicatethe conserved DDH triad of PIWI domain and the conserved H798 positions.
Fig 4.
RdRP conserved domain of the aa sequences of M. acuminata and Arabidopsis RDR proteins by Clustal-W program in MEGA 11.
The conserved DxDGD catalytic motif are surrounded by the red box.
Table 2.
Comparison of the AGO proteins in PIWI domains between M. acuminata and A. thaliana.
Fig 5.
Phylogenetic tree for (A) DCL proteins (B) AGO proteins and (C) RDR proteins from M. acuminata and Arabidopsis. All the phylogenetic trees were constructed using the neighbor-joining method and the numbers at the nodes indicate the percentages of bootstrap values from 1000 replications. The accession number and the abbreviations of proteins from M. acuminata are tabulated in (Table 1) while A. thaliana are given in section 2.1. In phylogenetic tree, different groups are represented by different colors; red circles are mentioned genes of M. acuminata and green circles are mentioned genes of A. thaliana.
Fig 6.
The conserved domains of the predicted MaDCL, MaAGO, and MaRDR proteins were drawn by Pfam database information.
Where, Helicase conserved C-terminal domain: Helicase-C; Dicer dimerization domain: Dicer-dimer; PAZ domain: PAZ; Ribonuclease III domain: RNase III; double-strand RNA binding domain from DEAD END PROTEIN 1: DND1-DSRM; DEAD/DEAH box helicase domain: DEAD; Double-stranded RNA binding motif: DSRM; Glycine-rich region of Argonaut: Gly-rich_Ago1; N-terminal domain of argonaute: ArgoN; Argonaute linker 1 domain: ArgoL1; Argonaute linker 2 domain: ArgoL2; Mid domain of argonaute: ArgoMid; PIWI domain: PIWI; Tify domain: Tify; CCT motif: CCT; GATA zinc finger: GATA; RNA dependent RNA polymerase: RdRP; Type III restriction enzyme domain: Res III.
Fig 7.
The conserved motifs of the predicted MaDCL, MaAGO and MaRDR protein families are drawn using MEME-suite (a maximum of 20 motifs are displayed).
Each color represents different motifs in the predicted proteins domains.
Fig 8.
Gene formation of the predicted MaDCL, MaAGO, and MaRDR proteins in M. acuminata with Arabidopsis by using Gene Structure Display Server (GSDS 2.0, http://gsds.cbi.pku.edu.cn/index.php) [76].
Fig 9.
The genomic location of the predicted MaDCL, MaAGO, and MaRDR genes.
The scale to indicate the chromosomal length is provided on the left. The ChrUn means the unknown chromosome.
Fig 10.
The Heatmap for the predicted GO terms corresponding to the predicted RNAi genes is represented for (A) biological process (B) cellular components and their association to the genes whether they are present or absent. The p-value corresponds to the GO terms are shown in the histogram adjacent to the Heatmap using−log10(p−value). The Ven diagrams are drawn to investigate the shared GO terms by MaDCL, MaAGO, and MaRDR gene families considering the (C) biological process (D) cellular components (E) molecular functions.
Fig 11.
Sub-cellular localization analysis for the (A) MaDCL, MaAGO, and MaRDR proteins. (B) The percentage of protein appeared in different cellular organelles. In this study, predicted proteins were analyzed in Nuclear, Mitochondrial, Cytoplasmic, Chloroplast, Cytoskeletal, Endoplasmic reticulum (ER), Plasma Membrane, Extracellular, Golgi, Lysosomal, Peroxisomal, and Vacuole.
Fig 12.
(A) The regulatory network among the TFs and the predicted RNAi genes. Each node of the network was colored based on RNAi genes and TFs. The MaDCL, MaAGO, and MaRDR genes were represented by pink, green, and blue node color, respectively, and the TFs were represented by yellow node color. Different node symbols were used for different families of TFs. TFs were configured at the hub node level using Magenta (B). The map represents the related number of TFs with the predicted MaRNAi genes.
Fig 13.
RNAi gene-mediated sub-network for ERF, Dof, C2H2, TCP, GATA and MIKC_MADS TFs families which is expressed as Heatmap.
Fig 14.
The CAREs in the upstream promoter region of predicted MaDCLs, MaAGOs and MaRDRs genes, respectively.
The deep color represents the presence of that element with the corresponding genes.