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Planta

, Volume 248, Issue 3, pp 729–743 | Cite as

Dicer-like and RNA-dependent RNA polymerase gene family identification and annotation in the cultivated Solanum tuberosum and its wild relative S. commersonii

  • Salvatore Esposito
  • Riccardo Aversano
  • Vincenzo D’Amelia
  • Clizia Villano
  • Daniela Alioto
  • Marie Mirouze
  • Domenico Carputo
Original Article

Abstract

Main conclusion

We provide advances in DCL and RDR gene diversity in Solanaceae. We also shed light on DCL and RDR gene expression in response to cold stress.

DICER-like (DCL) and RNA-dependent RNA polymerase (RDR) genes form the core components to trigger small non-coding RNA (ncRNA) production. In spite of this, little is known about the two gene families in non-model plant species. As their genome sequences are now available, the cultivated potato (Solanum tuberosum) and its cold-tolerant wild relative Solanum commersonii offer a valuable opportunity to advance our understanding of the above genes. To determine the extent of diversification and evolution of DCLs and RDRs in these species, we performed a comparative analysis. Seven DCLs were identified in the two species, whereas seven and six RDR genes were found in S. tuberosum and S. commersonii, respectively. Based on phylogenetic analysis with DCLs and RDRs from several species, we provide evidence for an increase in their number in both potato species. We also disclosed that tandem duplications played a major role in the evolution of these gene families in Solanaceae. DCL and RDR expression was investigated in different tissues and under cold and virus stresses, with divergent profiles of the tandem duplicated genes being found in different tissues. DCL paralogs showed a contrasting expression in S. tuberosum and S. commersonii following cold stress and virus infection. By contrast, no change in RDR transcript activity was detected following both stresses. Overall, this study provides the first comparative genomic analysis of the core components of the RNAi machinery in Solanaceae and offers a scaffold for future functional analysis of these gene families.

Keywords

Cold stress Comparative genomics Gene silencing MicroRNA biogenesis Potato virus Y 

Abbreviation

NACC

Non-acclimated conditions

ACC

Acclimated conditions

RDR

RNA-dependent RNA polymerases

DCL

Dicer-like

PAZ

Piwi/Argonaute/Zwille domain

Notes

Acknowledgements

This work was carried out within the project “Development of potato genetic resources for sustainable agriculture” (PORES) funded by the University of Naples Federico II. We thank R. Garramone and R. Nocerino for technical assistance and M. Walters for editing the manuscript. No conflict of interest declared.

Supplementary material

425_2018_2937_MOESM1_ESM.docx (563 kb)
Supplementary material 1 (DOCX 562 kb)

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Copyright information

© Springer-Verlag GmbH Germany, part of Springer Nature 2018

Authors and Affiliations

  1. 1.Department of Agricultural SciencesUniversity of Naples Federico IIPorticiItaly
  2. 2.Plant Genome and Development LaboratoryInstitut de Recherche pour le Développement, IRD DIADE, Université de PerpignanPerpignanFrance

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