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

Debasish B Krishnatreya,Tapan Kumar Mondal,Bhaskar Dowarah,Niraj Agarwala,Pooja Moni Baruah,Soni Chowrasia

doi:10.1038/s41598-021-87991-5

Debasish B Krishnatreya, Tapan Kumar Mondal + Show 4 more

Open Access

https://doi.org/10.1038/s41598-021-87991-5

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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.

Highlights

Gene regulation in eukaryotes depends on post-transcriptional RNA interference mechanisms which is mediated by the action of the small RNAs
Eighteen CsAGOs were identified after analysing against the pfam database for presence of the following AGO specific domains—Argo-N: N-terminal domain of AGO proteins; PAZ: a domain that anchors the 3′ end of the bound small RNA and Piwi_Ago-like: PIWI domain present in the C-terminal region
Five Dicer-like proteins (DCLs) and twelve RNA dependent RNA polymerase (RDRs) were identified in C. sinensis genome using Hidden Markov Model (HMM) profiles of gene specific conserved domains viz., RNaseIII, PAZ and dsRNA binding motif and RNA-dependent RNA polymerase (RdRP) followed by analysis against the pfam database

Summary

Introduction

Gene regulation in eukaryotes depends on post-transcriptional RNA interference mechanisms which is mediated by the action of the small RNAs (sRNAs). The RNA dependent RNA polymerases (RDRs) and Dicer-like proteins (DCLs) are directly involved in small RNA biogenesis, whereas Argonaute (AGO) constitutes a significant component of the RNA induced silencing complex (RISC)[3]. The sRNAs bind to specific AGO proteins and guide the RISC to their corresponding target genes through complementary base pairing between target mRNA and the guide strand of the sRNA. This mode of gene regulation may be mediated by two approaches, viz. Genome-wide analysis of the AGO, DCL and RDR gene families will decipher the diversity in these gene families and their function in this important commercial crop

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