The advance of tomato disease-related microRNAs

Wang, Weichen; Luan, Yushi

doi:10.1007/s00299-015-1782-0

Cited by 19 publications

(7 citation statements)

References 96 publications

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“…Here, via high-throughput sequencing, we found that 24 known and 7 novel miRNAs were significantly responsive to B. elliptica infection compared with their levels in the uninfected control. Among the differentially expressed miRNAs, the majority were downregulated under diseases stress, which is in accordance with findings in other species suffering biotic stress (Luo et al, 2015; Wang and Luan, 2015). For instance, including miR164, miR166, and miR168, the expression of these miRNAs were induced under Verticillium longisporum infection in Brassica napus (Shen et al, 2014), which were exhibit the same expression pattern in lily under B. elliptica -infection.…”

Section: Discussionsupporting

confidence: 88%

Transcriptome-Wide Analysis of Botrytis elliptica Responsive microRNAs and Their Targets in Lilium Regale Wilson by High-Throughput Sequencing and Degradome Analysis

Gao¹,

Cui²,

Cao³

et al. 2017

Front. Plant Sci.

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MicroRNAs, as master regulators of gene expression, have been widely identified and play crucial roles in plant-pathogen interactions. A fatal pathogen, Botrytis elliptica, causes the serious folia disease of lily, which reduces production because of the high susceptibility of most cultivated species. However, the miRNAs related to Botrytis infection of lily, and the miRNA-mediated gene regulatory networks providing resistance to B. elliptica in lily remain largely unexplored. To systematically dissect B. elliptica-responsive miRNAs and their target genes, three small RNA libraries were constructed from the leaves of Lilium regale, a promising Chinese wild Lilium species, which had been subjected to mock B. elliptica treatment or B. elliptica infection for 6 and 24 h. By high-throughput sequencing, 71 known miRNAs belonging to 47 conserved families and 24 novel miRNA were identified, of which 18 miRNAs were downreguleted and 13 were upregulated in response to B. elliptica. Moreover, based on the lily mRNA transcriptome, 22 targets for 9 known and 1 novel miRNAs were identified by the degradome sequencing approach. Most target genes for elliptica-responsive miRNAs were involved in metabolic processes, few encoding different transcription factors, including ELONGATION FACTOR 1 ALPHA (EF1a) and TEOSINTE BRANCHED1/CYCLOIDEA/PROLIFERATING CELL FACTOR 2 (TCP2). Furthermore, the expression patterns of a set of elliptica-responsive miRNAs and their targets were validated by quantitative real-time PCR. This study represents the first transcriptome-based analysis of miRNAs responsive to B. elliptica and their targets in lily. The results reveal the possible regulatory roles of miRNAs and their targets in B. elliptica interaction, which will extend our understanding of the mechanisms of this disease in lily.

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Section: Discussionsupporting

confidence: 88%

Transcriptome-Wide Analysis of Botrytis elliptica Responsive microRNAs and Their Targets in Lilium Regale Wilson by High-Throughput Sequencing and Degradome Analysis

Gao¹,

Cui²,

Cao³

et al. 2017

Front. Plant Sci.

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“…Differential miRNA expression analysis indicated that both conserved and Solanaceae-specific miRNAs were differentially regulated during Alternaria stress, which is analogous to observations with other plant–pathogen interaction studies 4 , 18 , 22 , 23 . Our stringent analysis demonstrated that majority of miRNAs were down-regulated upon Alternaria- stress.…”

Section: Discussionsupporting

confidence: 86%

Integrated miRNA and mRNA expression profiling reveals the response regulators of a susceptible tomato cultivar to early blight disease

et al. 2017

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Early blight, caused by the fungus Alternaria solani, is a devastating foliar disease of tomatoes, causes massive yield loss each year worldwide. Molecular basis of the compatible host–pathogen interaction was elusive. We adopted next generation sequencing approach to decipher miRNAs and mRNAs that are differentially expressed during Alternaria-stress in tomato. Some of the interesting findings were also validated by alternative techniques. Our analysis revealed 181 known-miRNAs, belonging to 121 miRNA families, of which 67 miRNAs showed at least 2-fold change in expression level with the majority being downregulated. Concomitantly, 5,450 mRNAs were significantly regulated in the same diseased tissues. Differentially expressed genes were most significantly associated with response to stimulus process, photosynthesis, biosynthesis of secondary metabolites, plant–pathogen interaction and plant hormone signal transduction pathways. GO term enrichment-based categorization of gene-functions further supported this observation, as terms related to pathogen perception, disease signal transduction, cellular metabolic processes including oxidoreductase and kinase activity were over represented. In addition, we have discovered 102 miRNA–mRNA pairs which were regulated antagonistically, and careful study of the targeted mRNAs depicted that multiple transcription factors, nucleotide-binding site leucine-rich repeats, receptor-like proteins and enzymes related to cellular ROS management were profoundly affected. These studies have identified key regulators of Alternaria-stress response in tomato and the subset of genes that are likely to be post-transcriptionally silenced during the infection.

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“…Data from the present work also show significant changes in expression profiles of miRNAs controlling various classes of R genes including NLRs (TIR-NBS-LRR and CC-NBS-LRR), RLPs, and RLKs. Upon PVY infection, miR482, miR6022, miR6023, miR6024, and miR6027 families, known for targeting R genes in tomato [81][82][83], were found to be either up-or down-regulated in our libraries. Sly-miR6023 and sly-miR6024 were here validated as post-transcriptional regulators of Cf-9 and R1A-4, respectively.…”

Section: Discussionmentioning

confidence: 91%

Potato Virus Y Infection Alters Small RNA Metabolism and Immune Response in Tomato

Prigigallo

Križnik

Paola³

et al. 2019

Viruses

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Potato virus Y (PVY) isolate PVYC-to induces growth reduction and foliar symptoms in tomato, but new vegetation displays symptom recovery at a later stage. In order to investigate the role of micro(mi)RNA and secondary small(s)RNA-regulated mechanisms in tomato defenses against PVY, we performed sRNA sequencing from healthy and PVYC-to infected tomato plants at 21 and 30 days post-inoculation (dpi). A total of 792 miRNA sequences were obtained, among which were 123 canonical miRNA sequences, many isomiR variants, and 30 novel miRNAs. MiRNAs were mostly overexpressed in infected vs. healthy plants, whereas only a few miRNAs were underexpressed. Increased accumulation of isomiRs was correlated with viral infection. Among miRNA targets, enriched functional categories included resistance (R) gene families, transcription and hormone factors, and RNA silencing genes. Several 22-nt miRNAs were shown to target R genes and trigger the production of 21-nt phased sRNAs (phasiRNAs). Next, 500 phasiRNA-generating loci were identified, and were shown to be mostly active in PVY-infected tissues and at 21 dpi. These data demonstrate that sRNA-regulated host responses, encompassing miRNA alteration, diversification within miRNA families, and phasiRNA accumulation, regulate R and disease-responsive genes. The dynamic regulation of miRNAs and secondary sRNAs over time suggests a functional role of sRNA-mediated defenses in the recovery phenotype.

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The advance of tomato disease-related microRNAs

Cited by 19 publications

References 96 publications

Transcriptome-Wide Analysis of Botrytis elliptica Responsive microRNAs and Their Targets in Lilium Regale Wilson by High-Throughput Sequencing and Degradome Analysis

Transcriptome-Wide Analysis of Botrytis elliptica Responsive microRNAs and Their Targets in Lilium Regale Wilson by High-Throughput Sequencing and Degradome Analysis

Integrated miRNA and mRNA expression profiling reveals the response regulators of a susceptible tomato cultivar to early blight disease

Potato Virus Y Infection Alters Small RNA Metabolism and Immune Response in Tomato

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