Tomato MicroRNAs and Their Functions

Arazi, Tzahi; Khedia, Jackson

doi:10.3390/ijms231911979

Cited by 12 publications

(7 citation statements)

References 121 publications

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“…Differences in sensitivities between the two techniques have also been observed for the tomato-plant responses to different biotic and abiotic stresses [53]. Among the seven known DE miRNAs, there were six (miR166a, miR398, miR408, and miR6027 were downregulated and miR5300 and miR6024 were upregulated) that had previously been linked to stress responses and development in tomato plants [54][55][56].…”

Section: Discussionmentioning

confidence: 94%

Identification of Tomato microRNAs in Late Response to Trichoderma atroviride

Olmo,

Quijada,

Morán-Diez

et al. 2024

IJMS

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The tomato (Solanum lycopersicum) is an important crop worldwide and is considered a model plant to study stress responses. Small RNAs (sRNAs), 21–24 nucleotides in length, are recognized as a conserved mechanism for regulating gene expression in eukaryotes. Plant endogenous sRNAs, such as microRNA (miRNA), have been involved in disease resistance. High-throughput RNA sequencing was used to analyze the miRNA profile of the aerial part of 30-day-old tomato plants after the application of the fungus Trichoderma atroviride to the seeds at the transcriptional memory state. Compared to control plants, ten differentially expressed (DE) miRNAs were identified in those inoculated with Trichoderma, five upregulated and five downregulated, of which seven were known (miR166a, miR398-3p, miR408, miR5300, miR6024, miR6027-5p, and miR9471b-3p), and three were putatively novel (novel miR257, novel miR275, and novel miR1767). miRNA expression levels were assessed using real-time quantitative PCR analysis. A plant sRNA target analysis of the DE miRNAs predicted 945 potential target genes, most of them being downregulated (84%). The analysis of KEGG metabolic pathways showed that most of the targets harbored functions associated with plant–pathogen interaction, membrane trafficking, and protein kinases. Expression changes of tomato miRNAs caused by Trichoderma are linked to plant defense responses and appear to have long-lasting effects.

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Section: Discussionmentioning

confidence: 94%

Identification of Tomato microRNAs in Late Response to Trichoderma atroviride

Olmo,

Quijada,

Morán-Diez

et al. 2024

IJMS

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“…Around 28.2% of these miRNAs were conserved in other plant species, 9.6% were solanaceous-specific, and 13.3% were S. lycopersicum -specific. Moreover, we found unique unannotated miRNAs (46.4%) that belonged to 22 known families (miRNA isoforms) and 2 unannotated miRNAs that belong to the new sly-miR1-5p family (Table 2 , Dataset S11) [ 75 , 76 ]. The sly-miR166 family was the one with the highest number of expressed miRNAs in our dataset (Fig.…”

Section: Resultsmentioning

confidence: 99%

Transcriptional and epigenetic changes during tomato yellow leaf curl virus infection in tomato

Romero-Rodríguez,

Petek,

Jiao

et al. 2023

BMC Plant Biol

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Background Geminiviruses are DNA plant viruses that cause highly damaging diseases affecting crops worldwide. During the infection, geminiviruses hijack cellular processes, suppress plant defenses, and cause a massive reprogramming of the infected cells leading to major changes in the whole plant homeostasis. The advances in sequencing technologies allow the simultaneous analysis of multiple aspects of viral infection at a large scale, generating new insights into the molecular mechanisms underlying plant-virus interactions. However, an integrative study of the changes in the host transcriptome, small RNA profile and methylome during a geminivirus infection has not been performed yet. Using a time-scale approach, we aim to decipher the gene regulation in tomato in response to the infection with the geminivirus, tomato yellow leaf curl virus (TYLCV). Results We showed that tomato undergoes substantial transcriptional and post-transcriptional changes upon TYLCV infection and identified the main altered regulatory pathways. Interestingly, although the principal plant defense-related processes, gene silencing and the immune response were induced, this cannot prevent the establishment of the infection. Moreover, we identified extra- and intracellular immune receptors as targets for the deregulated microRNAs (miRNAs) and established a network for those that also produced phased secondary small interfering RNAs (phasiRNAs). On the other hand, there were no significant genome-wide changes in tomato methylome at 14 days post infection, the time point at which the symptoms were general, and the amount of viral DNA had reached its maximum level, but we were able to identify differentially methylated regions that could be involved in the transcriptional regulation of some of the differentially expressed genes. Conclusion We have conducted a comprehensive and reliable study on the changes at transcriptional, post-transcriptional and epigenetic levels in tomato throughout TYLCV infection. The generated genomic information is substantial for understanding the genetic, molecular and physiological changes caused by TYLCV infection in tomato.

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“…Plant genome possess conserved small non-coding microRNAs genes, which play important roles in gene regulation at various life stages of plant (Arazi et al 2022;Guo et al 2022;Teotia et al 2023). High conserved nature of miRNAs existed among different organisms (Islam et al 2022;Pei et al 2023).…”

Section: Discussionmentioning

confidence: 99%

Molecular mechanism of flower color formation in Rhododendron simsii Planchon revealed by integration of microRNAome and RNAomics

Wu,

Wan,

Huang

et al. 2023

Preprint

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Background Systems-wide understanding of gene regulatory networks underlying flower color formation in Rhododendron simsii is insufficient. In this research, integration analysis of microRNAome and RNAomics were performed to reveal the molecular mechanism of flower color formation in three R. simsii varieties with red, pink, and crimson flowers, respectively. Results A total of 213 miRNAs, containing 151 known miRNAs belonging to 55 families and 62 novel miRNA, were identified. In particular, 53 miRNAs were significantly differently expressed. The top significant enriched GO terms were mainly “meristem maintenance”, “carbohydrate metabolic process”, and “signal transduction”. The main KEGG pathways were “Monobactam biosynthesis”, “Plant-pathogen interaction”, and “MAPK signaling pathway-plant”. The miRNA–mRNA regulatory network construction showed that key genes and pathways were mainly associated with synthesis of secondary metabolites. In particular, ath-miR5658 could affect the synthesis of pelargonidin, cyanidin, and delphinidin through downregulating expression of anthocyanidin 3-O-glucosyltransferase; ath-miR868-3p could regulate isoflavonoid biosynthesis through downregulating expression of CYP81E1/E7; ath-miR156g regulated the expression of flavonoid 3',5'-hydroxylase; ath-miR829-5p regulated flavonol synthase in flavonoid biosynthesis process. Conclusion This research will provide critical clues of flower color formation, and provide novel insights into the breeding of new varieties with rich flower color.

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Tomato MicroRNAs and Their Functions

Cited by 12 publications

References 121 publications

Identification of Tomato microRNAs in Late Response to Trichoderma atroviride

Identification of Tomato microRNAs in Late Response to Trichoderma atroviride

Transcriptional and epigenetic changes during tomato yellow leaf curl virus infection in tomato

Molecular mechanism of flower color formation in Rhododendron simsii Planchon revealed by integration of microRNAome and RNAomics

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