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

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.

Coffee microsporogenesis and related small interfering RNAs biosynthesis have a unique pattern among eudicots suggesting a sensitivity to climate changes

“…S1); two DCL3 copies were found to be similar in sequence but from different parental subgenomes; and finally, only one CaDCL4 copy was found, from the C. eugenioides' subgenome (Table S1). Compared to other works, here we found five more DCLs than previously described by Mosharaf et al (2019) and eight more than those published by Noronha Fernandes-Brum et al (2017). Details of all the sequences are available in Table S1.…”

Microsporogenesis and the biosynthesis of floral small interfering RNAs in coffee have a unique pattern among eudicots, suggesting a sensitivity to climate changes

“…The DCL2 clade was the group with the highest number of CaDCLs homologs, eight, but only CaDCL2.1 presented the complete main domains (Table S1 and Figure S1); two DCL3 copies were found to be similar in sequence but from different parental subgenomes; and finally, only one CaDCL4 copy was found, from the C. eugenioides ' subgenome (Table S1). Compared to other works, here we found five more DCLs than previously described by Mosharaf et al (2019) and eight more than those published by Noronha Fernandes‐Brum et al (2017). Details of all the sequences are available in Table S1.…”

Comparative Analysis and Function of Multiprotein Bridging Factor1 (MBF1) Genes in Cotton

“…The analysis also suggested a significant difference in the enrichment of cis-regulatory elements in MBF1c genes including TGA-element, AT-rich sequence, wun-motif, AuxRR-core and telo-motif respectively. Studies suggested that the identified cis-regulatory elements play important role in cotton fiber development, transcriptional activity of genes as well as in response to drought stress (Huang et al 2020;Li et al 2006;Mosharaf et al 2019;Tjaden and Coruzzi 1994). These results evidenced the MBF1 family genes are highly conserved with important cis-regulatory elements.…”