Genome-wide identification, evolutionary relationship and expression

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, 5DCLs 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 ofCsAGO4, which are known to participate in biogenesis of hc-siRNAs, showed similarities in their expression levels in most of the tea plant tissues.

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Fig: Phylogenetic trees showing relationships between (A) AGOs, (B) DCLs and (C) RDRs of C. sinensis and A. thaliana. The trees were constructed using the maximum likelihood method and a bootstrap replicate of 1000. The trees with the highest bootstrap support for each gene class have been shown here.

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.

Krishnatreya, D.B., Baruah, P.M., Dowarah, B. et al. Genome-wide identification, evolutionary relationship and expression analysis ofAGO, DCL and RDR family genes in tea. Sci Rep 11, 8679 (2021). https://doi.org/10.1038/s41598-021-87991-5

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