Genome-wide identification, characterization and phylogenetic analysis of Dicer-like (DCL) gene family in Coffea arabica.

Md Parvez Mosharaf

doi:10.6026/97320630015824

Abstract

A fine-tuned RNA interference (RNAi) pathway has been developed by plants to restrain distinct biological processes in various life stages including stress responses, development and maintenance of genome integrity. The Dicer-Like (DCL) proteins starts the RNAi process by producing complementary double-stranded RNAs (dsRNAs) into small RNA duplexes (21-24 nucleotides) trigger the RNAi process. Nevertheless, these members of RNAi pathway have not been deciphered in one of the most economically important plant coffee (Coffea arabica). Therefore, it is of interest to report the identification and phylogenetic analysis of the DCL genes in C. arabica. We report 5 DCL genes and categorized them into three significant groups to interpret the evolutionary relationship with DCLs of the model plant Arabidopsis thaliana. Moreover, the subcellular location of the reported DCL proteins and the associated cis-acting regulatory elements were also identified and discussed in this report. The cis-regulatory elements indicated the biological and molecular functional diversity of the identified DCL genes related with plant growth and development. The present findings will provide a better basis for further experimental research on RNAi pathway genes in C. arabica.

Highlights

Plants have developed a fine-tuned RNA interference (RNAi) pathway to regulate various biological processes, including development, stress responses and maintenance of genome integrity
Result and Discussion: To identify the RNAi pathway genes in C. arabica, all the downloaded sequences were examinedto check their properties compared to the Arabidopsis DCLs.Finally5CaDCL genes were recognized in the coffee genome
The evolutionary relationship study revealed that the DCL3 and DCL4 have two more members, which are named as CaDCL3b and CaDCL4b (Figure 2)

Summary

Introduction

Plants have developed a fine-tuned RNA interference (RNAi) pathway to regulate various biological processes, including development, stress responses and maintenance of genome integrity. In plants most of the biological and molecular functions are triggered by two types of small RNA called microRNA (miRNA) and short interfering RNA (siRNA) [1, 2] These small RNA contain 21-24 nucleotides, which are involved with both transcriptional and post-transcriptional RNA mediated gene silencing [3]. The DCL, AGO and RDR gene families contain multiple genes belonging to distinct RNAi pathways [8, 9] These RNAi genes have been characterized in many species with their functional activities, which helps to make genetic development for those plants. In silico identification of RNAi genes in many species had been conducted before [17]

Methods

Findings

Discussion

Conclusion