Integrative Analysis of the DICER-like (DCL) Genes From Peach (Prunus persica): A Critical Role in Response to Drought Stress

Abstract

DICER-likes (DCLs) proteins are the core component for non-coding RNA (ncRNA) biogenesis, playing essential roles in some biological processes. The DCL family has been characterized in model plants, such as Arabidopsis, rice, and poplar. However, the evolutionary aspect and the expression mechanism under drought stress were scarce and have never been reported and characterized in one of the most important worldwide cultivated fruit trees, peach (Prunus persica). Eight DCLs genes in the Prunus persica genome were detected, in addition to 51 DCLs in the other seven Rosaceae genomes. The phylogenetic analysis with Arabidopsis thaliana and RTL1 gene as outgroups suggested that DCL members are divided into four clades: DCL1, DCL2, DCL3, and DCL4 with several gene gain/loss events of DCL gene copies through the evolutionary tract of the Rosacea family. The number of homologous DCL copies within each clade, along with the chromosomal location indicated gene duplication event of the DCL2 gene occurred once for the subfamily Amygdaloideae and twice for Pyrus communis and Prunus dulics and trice for the P. persica on Chromosome number 7 genes. Another duplication event was found for the DCL3 gene that occurred once for all the eight Rosaceae species with no match in A. thaliana. The DCL genetic similarity and activity was evaluated using BLASTp and previously published RNA-seq data among different tissues and over different time points of peach trees exposed to drought conditions. Finally, the expression pattern of PrupeDCLs in response to drought stress was identified, and two of these members, Prupe.7G047900 and Prupe.6G363600, were found as main candidate genes for response to drought stress. Our data presented here provide useful information for a better understanding of the molecular evolution of DCL genes in Rosaceae genomes, and the function of DCLs in P. persica.

Systematic genome-wide and expression analysis of RNA-directed DNA methylation pathway genes in grapes predicts their involvement in multiple biological processes

“…Our results are also supported by the earlier findings i.e., the activity of DCL2 in A. thaliana was related with temperature (Zhang et al, 2012). Prupe DCL under drought treatment was differentially expressed in peach (Belal et al, 2022). These findings suggest, that the functions of DCL2 are diverse, and further research is needed for exploring the exact functions of VvDCL2.…”

Genome-wide analysis of key gene families in RNA silencing and their responses to biotic and drought stresses in adzuki bean

“…Upregulation of SsDCL1a/2/3, SsRDR3/6b and SsAGO2b/5a/5c/6b/SsAGO10c [ 46 ], ZmDCL2/3b, ZmAGO4a/4d/7, ZmRDR2/4 [ 48 ], CaDCL1/2/3, CaRDR2/6, and CaAGO2/10b [ 49 ] was observed under drought stress. In our study, four DCLs were significantly upregulated and two (VaDCL2c in DS and VaDCL3 in DR) were downregulated, similar to the expression pattern in peach [ 47 ]. Several AGOs were induced while VaAGO4a was depressed in the DS genotype (Fig.…”

Genome-Wide Identification and Characterization of Argonaute, Dicer-like and RNA-Dependent RNA Polymerase Gene Families and Their Expression Analyses in Fragaria spp.

“…In pepper, CaDCL1 and CaDCL3 also exhibited a higher expression in flowers [21], and previous studies revealed that the double mutant of dcl1 and dcl3 exhibited a delay in the flowing of Arabidopsis [109]. Additionally, in peach, PrupeDCL3 also showed a high level of expression in flowers [63]. These findings suggest that DCL1 and DCL3 play positive roles in the flower development of plants.…”

“…For vegetable crops, seven DCLs have been identified in tomato [25], four in pepper [21], six in common bean [61], eight in Brassica napus [33], and eleven in allotetraploid cotton [62]. Moreover, DCLs were also found in the fruit crops, including grape (four DCLs) [22], sweet orange (five DCLs) [23], banana (three DCLs) [24], and peach (eight DCLs) [63].…”