Genome-wide identification of Argonautes in Solanaceae with emphasis on potato

Zhen Liao,Ravi Kumar Singh,Kristian Persson Hodén,Christina Dixelius

doi:10.1038/s41598-020-77593-y

Zhen Liao, Ravi Kumar Singh + Show 2 more

Open Access

https://doi.org/10.1038/s41598-020-77593-y

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Abstract

Regulatory small RNAs (sRNAs) play important roles in many fundamental processes in plant biology such as development, fertilization and stress responses. The AGO protein family has here a central importance in gene regulation based on their capacity to associate with sRNAs followed by mRNA targeting in a sequence-complementary manner. The present study explored Argonautes (AGOs) in the Solanaceae family, with emphasis on potato, Solanum tuberosum (St). A genome-wide monitoring was performed to provide a deeper insight into gene families, genomic localization, gene structure and expression profile against the potato late blight pathogen Phytophthora infestans. Among 15 species in the Solanaceae family we found a variation from ten AGOs in Nicotiana obtusifolia to 17 in N. tabacum. Comprehensive analyses of AGO phylogeny revealed duplication of AGO1, AGO10 and AGO4 paralogs during early radiation of Solanaceae. Fourteen AGOs were identified in potato. Orthologs of AGO8 and AGO9 were missing in the potato genome. However, AGO15 earlier annotated in tomato was identified. StAGO15 differs from the other paralogs having residues of different physico-chemical properties at functionally important amino acid positions. Upon pathogen challenge StAGO15 was significantly activated and hence may play a prominent role in sRNA-based regulation of potato defense.

Highlights

Regulatory small RNAs play important roles in many fundamental processes in plant biology such as development, fertilization and stress responses
Maximum losses have occurred in N. benthamiana (20) followed by N. tabacum (15)
Genes were detected enriched in the genomes either by whole genome duplication or by tandem duplication

Summary

Introduction

Regulatory small RNAs (sRNAs) play important roles in many fundamental processes in plant biology such as development, fertilization and stress responses. The AGO protein family has here a central importance in gene regulation based on their capacity to associate with sRNAs followed by mRNA targeting in a sequence-complementary manner. The core part required for this regulatory RNA-based process involves canonical ribonucleases that participate in initiator and effector steps They are Dicer or DICER-LIKE (DCL) proteins that cleave double-stranded RNA and Argonautes (AGOs), important for the small RNA association and formation of the RNA-induced RNA silencing complexes (RISCs)[2,3]. Eukaryotic AGO proteins are characterized by four domains of importance to bind diverse sRNA classes. They are: PAZ (Piwi-Argonaute-Zwille), MID, PIWI, and N-terminal sequences[5]. The Solanaceae gene families vary in size due to duplications and different gene evolutionary e vents[24]

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