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

Autor: Salvatore Esposito, Domenico Carputo, Clizia Villano, Daniela Alioto, Riccardo Aversano, Marie Mirouze, Vincenzo D'Amelia
Přispěvatelé: Esposito, S, Aversano, R, D'Amelia, V, Villano, C, Alioto, D, Mirouze, M, Carputo, D, Department of Agricultural Sciences, Division of Grape and Wine Sciences, Università degli studi di Napoli Federico II, Department of Agriculture, Dipartimento di Agraria, University of Sassari, Diversité, adaptation, développement des plantes (UMR DIADE), Institut de Recherche pour le Développement (IRD [France-Sud])-Centre National de la Recherche Scientifique (CNRS)-Université de Montpellier (UM)-Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad), Department of Agricultural Sciences, Division of Plant Genetics and Biotechnology
Rok vydání: 2018
Předmět:
Zdroj: Planta
Planta, Springer Verlag, 2018, 248 (3), pp.729-743. ⟨10.1007/s00425-018-2937-3⟩
ISSN: 1432-2048
0032-0935
DOI: 10.1007/s00425-018-2937-3⟩
Popis: 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.
Databáze: OpenAIRE
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