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

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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.

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Abbreviations

NACC:

Non-acclimated conditions

ACC:

Acclimated conditions

RDR:

RNA-dependent RNA polymerases

DCL:

Dicer-like

PAZ:

Piwi/Argonaute/Zwille domain

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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.

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Authors and Affiliations

  1. Department of Agricultural Sciences, University of Naples Federico II, Via Università 100, Portici, Italy

    Salvatore Esposito, Riccardo Aversano, Vincenzo D’Amelia, Clizia Villano, Daniela Alioto & Domenico Carputo

  2. Plant Genome and Development Laboratory, Institut de Recherche pour le Développement, IRD DIADE, Université de Perpignan, Perpignan, France

    Marie Mirouze

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  1. Salvatore Esposito
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  2. Riccardo Aversano
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  3. Vincenzo D’Amelia
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  6. Marie Mirouze
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  7. Domenico Carputo
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Correspondence to Riccardo Aversano or Domenico Carputo.

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Esposito, S., Aversano, R., D’Amelia, V. et al. Dicer-like and RNA-dependent RNA polymerase gene family identification and annotation in the cultivated Solanum tuberosum and its wild relative S. commersonii. Planta 248, 729–743 (2018). https://doi.org/10.1007/s00425-018-2937-3

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