Genome-wide identification, evolutionary relationship and expression analysis of AGO, DCL and RDR family genes in tea

Abstract

Three gene families in plants viz. Argonaute (AGOs), Dicer-like (DCLs) and RNA dependent RNA polymerase (RDRs) constitute the core components of small RNA mediated gene silencing machinery. The present study endeavours to identify members of these gene families in tea and to investigate their expression patterns in different tissues and various stress regimes. Using genome-wide analysis, we have identified 18 AGOs, 5 DCLs and 9 RDRs in tea, and analyzed their phylogenetic relationship with orthologs of Arabidopsis thaliana. Gene expression analysis revealed constitutive expression of CsAGO1 in all the studied tissues and stress conditions, whereas CsAGO10c showed most variable expression among all the genes. CsAGO10c gene was found to be upregulated in tissues undergoing high meristematic activity such as buds and roots, as well as in Exobasidium vexans infected samples. CsRDR2 and two paralogs of CsAGO4, which are known to participate in biogenesis of hc-siRNAs, showed similarities in their expression levels in most of the tea plant tissues. This report provides first ever insight into the important gene families involved in biogenesis of small RNAs in tea. The comprehensive knowledge of these small RNA biogenesis purveyors can be utilized for tea crop improvement aimed at stress tolerance and quality enhancement.

A ribose world: current status and future challenges of plant RNA biology

“…dsRNAs are a potent trigger for cellular pathogen defence pathways of plant cells, namely RNA interference. The Arabidopsis genome contains six RDRs linked to the silencing of distinct target RNAs ( Willmann et al , 2011 ), but the copy number varies across plant species ( Krishnatreya et al , 2021 ). RDR activity can also start from ssRNA, where it can be primed by 22-nucleotide small RNAs (sRNAs), resulting in secondary sRNA production from an initial sRNA trigger for the cellular amplification of silencing ( Lopez-Gomollon and Baulcombe, 2022 ).…”

Extracellular vesicles: Their functions in plant–pathogen interactions

“…This finding suggests that sRNAs are selectively loaded by host plants into EVs during pathogen infection. In eukaryotes, Argonaute (AGO) proteins bind selectively to specific sRNAs and then guide the RNA‐induced silencing complex to corresponding target genes by complementary base pairing between the target mRNA and the sRNA guide strand (Krishnatreya et al, 2021 ; Liu et al, 2017 ). To elucidate the mechanism underlying selective loading of RNAs into EVs by plants, He et al ( 2021 ) used proteomic analysis to identify various RNA‐binding proteins in Arabidopsis EVs; these included AGO1, DEAD‐box RNA helicases (RH11, RH37), and annexins (ANN1, ANN2).…”

Genome-wide identification, characterization and expression analysis of AGO, DCL, and RDR families in Chenopodium quinoa

“…To date, several studies have shown that the sizes of AGO , DCL , and RDR gene families vary among species. For example, Arabidopsis 14 , rice 15 , maize 16 , millet 17 , grapevine 18 , tomato 19 , wheat 20 , soybean 21 , pepper 22 , cucumber 23 , barley 24 , sugarcane 25 , sweet orange 6 , and tea 26 genomes encode ten, 19, 18, 19, 13, 15, 39, 21, 12, seven, 11, 21, eight, and 18 AGO genes; four, five, five, eight, four, seven, seven, seven, four, five, five, four, four, and five DCL genes; six, eight, five, 11, five, six, 16, seven, six, eight, seven, 11, four, and nine RDR genes, respectively. These studies have also shown that these gene families are highly conserved in plants, although little is known about the corresponding genes in quinoa.…”