Sly-miR166 and Sly-miR319 are components of the cold stress response in Solanum lycopersicum

Valiollahi, Ehsan; Farsi, Mohammad; Kakhki, Amin Mirshamsi

doi:10.1007/s11816-014-0326-3

Cited by 38 publications

(21 citation statements)

References 60 publications

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“…After experimental verification, two of these TYLCV-responsive lncRNAs were confirmed to be target mimics of miR166 and miR399. miR166 is a well-studied plant miRNA involved in various aspects of plant development 62 , abiotic stresses such as drought and cold stresses 63 64 , and biotic stress such as fungal invision 65 66 . In wheat, miR166a and miR166d were significantly altered after powdery mildew infection 65 .…”

Section: Discussionmentioning

confidence: 99%

Genome-wide analysis of tomato long non-coding RNAs and identification as endogenous target mimic for microRNA in response to TYLCV infection

Wang

Yang

et al. 2015

Sci Rep

178

139

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Recently, a large number of long noncoding RNAs (lncRNAs) have emerged as important regulators of many biological processes in animals and plants. However, how lncRNAs function during plant DNA virus infection is largely unknown. We performed strand-specific paired-end RNA sequencing of tomato samples infected with Tomato yellow leaf curl virus (TYLCV) with three biological replicates. Overall, we predicted 1565 lncRNAs including long intergenic ncRNAs (lincRNAs) and natural antisense transcripts (lncNATs) and definitively identified lnRNAs that are involved in TYLCV infection by virus-induced gene silencing (VIGS). We also verified the functions of a set of lncRNAs that were differentially expressed between 0 and 7 days post inoculation (dpi). More importantly, we found that several lncRNAs acted as competing endogenous target mimics (eTMs) for tomato microRNAs involved in the TYLCV infection. These results provide new insight into lncRNAs involved in the response to TYLCV infection that are important components of the TYLCV network in tomatoes.

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Section: Discussionmentioning

confidence: 99%

Genome-wide analysis of tomato long non-coding RNAs and identification as endogenous target mimic for microRNA in response to TYLCV infection

Wang

Yang

et al. 2015

Sci Rep

178

139

View full text Add to dashboard Cite

show abstract

“…Up-regulation of miR319a under both cold stress treatments in the two studied varieties was observed. Other studies have also noted the over-expression of miR319 under cold stress treatments [ 29 , 51 , 52 ]. The members of this miRNA family are usually up-regulated when plants are exposed to different stresses [ 53 ].…”

Section: Discussionmentioning

confidence: 91%

The Small-RNA Profiles of Almond (Prunus dulcis Mill.) Reproductive Tissues in Response to Cold Stress

et al. 2016

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Spring frost is an important environmental stress that threatens the production of Prunus trees. However, little information is available regarding molecular response of these plants to the frost stress. Using high throughput sequencing, this study was conducted to identify differentially expressed miRNAs, both the conserved and the non-conserved ones, in the reproductive tissues of almond tolerant H genotype under cold stress. Analysis of 50 to 58 million raw reads led to identification of 174 unique conserved and 59 novel microRNAs (miRNAs). Differential expression pattern analysis showed that 50 miRNA families were expressed differentially in one or both of almond reproductive tissues (anther and ovary). Out of these 50 miRNA families, 12 and 15 displayed up-regulation and down-regulation, respectively. The distribution of conserved miRNA families indicated that miR482f harbor the highest number of members. Confirmation of miRNAs expression patterns by quantitative real- time PCR (qPCR) was performed in cold tolerant (H genotype) alongside a sensitive variety (Sh12 genotype). Our analysis revealed differential expression for 9 miRNAs in anther and 3 miRNAs in ovary between these two varieties. Target prediction of miRNAs followed by differential expression analysis resulted in identification of 83 target genes, mostly transcription factors. This study comprehensively catalogued expressed miRNAs under different temperatures in two reproductive tissues (anther and ovary). Results of current study and the previous RNA-seq study, which was conducted in the same tissues by our group, provide a unique opportunity to understand the molecular basis of responses of almond to cold stress. The results can also enhance the possibility for gene manipulation to develop cold tolerant plants.

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“…All of these miRNAs were up-regulated in response to chilling stress (Table 1 ). In other plant species, miR156, miR166, miR169 and miR172 were also found to be significantly responsive to chilling stress 24 – 28 . In this study, we also found that chilling stress induced the aberrant expression of miR403.…”

Section: Discussionmentioning

confidence: 96%

High throughput deep sequencing reveals the important roles of microRNAs during sweetpotato storage at chilling temperature

Xie

Wang

et al. 2017

Sci Rep

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Sweetpotato (Impomoea batatas L.) is a globally important economic food crop with a potential of becoming a bioenergy and pharmaceutical crop. Thus, studying the molecular mechanism of tuberous root development and storage is very important. However, not too much progress has been made in this field. In this study, we employed the next generation high-throughput deep sequencing technology to sequence all small RNAs and degradome of sweetpotato for systematically investigating sweetpotato response to chilling stress during storage. A total of 190 known microRNAs (miRNAs) and 191 novel miRNAs were identified, and 428 transcripts were targeted by 184 identified miRNAs. More importantly, we identified 26 miRNAs differentially expressed between chilling stress and control conditions. The expression of these miRNAs and their targets was also confirmed by qRT-PCR. Integrated analysis of small RNAs and degradome sequencing reveals that miRNA-mediated SA signaling, ABA-dependent, and ROS response pathways are involved in sweetpotato root response to chilling stress during storage.

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Sly-miR166 and Sly-miR319 are components of the cold stress response in Solanum lycopersicum

Cited by 38 publications

References 60 publications

Genome-wide analysis of tomato long non-coding RNAs and identification as endogenous target mimic for microRNA in response to TYLCV infection

Genome-wide analysis of tomato long non-coding RNAs and identification as endogenous target mimic for microRNA in response to TYLCV infection

The Small-RNA Profiles of Almond (Prunus dulcis Mill.) Reproductive Tissues in Response to Cold Stress

High throughput deep sequencing reveals the important roles of microRNAs during sweetpotato storage at chilling temperature

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