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

Abstract

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.

WRKY genes family study reveals tissue-specific and stress-responsive TFs in wild potato species

“…Interestingly, two ScWRKYs (ScWRKY010 and ScWRKY002) carried three WDs. This might be the result of the acquisition of a WRKY domain during evolution, supporting findings of Aversano et al 15 and Esposito et al 31,55 , who reported that S. commersonii prosper lineage-specific segmental duplications during evolution. Not only WDs number, but also WDs structural divergences identified in S. commersonii and S. chacoense might be the consequence of mutations during the process of evolution.…”

“…Three-week-old seedlings were used for all stress experiments and sampled in a 0, 1, 2, 4, 6 hpt (hours post treatment) time course. As for virus infection, young plants of clone cmm1T were mechanically inoculated with Potato Virus Y tuber necrotic strain (PVY NTN ) as reported by Esposito et al 31 . For assessing bacterial resistance, the protocol of Melito et al 32 was used with few modifications.…”

Genome-Wide HMG Family Investigation and Its Role in Glycoalkaloid Accumulation in Wild Tuber-Bearing Solanum commersonii

“…It is particularly attractive for its freezing tolerance and capacity to cold acclimate [23]. Furthermore, it is the first wild potato whose genome sequence has been released [23], paving the way to different studies aimed to gain insights into genomic evolution at the sequence level from the wild to the cultivated form [24,25]. S. commersonii possesses a diverse mixture of glycoalkaloids, such as dehydrotomatine, dehydrodemissine and dehydrocommersonine, which are among the most poisonous compounds against different potato pests [26].…”

Deep‐sequencing of Solanum commersonii small RNA libraries reveals riboregulators involved in cold stress response

“…; Esposito et al . ). Therefore, it represents a significant resource to uncover the molecular regulation controlling tolerance to low temperatures and capacity to cold acclimate.…”