New insights into tomato microRNAs

Cardoso, Thaís Cunha de Sousa; Alves, Tamires Caixeta; Caneschi, Carolina Milagres; Santana, Douglas dos Reis Gomes; Fernandes-Brum, Christiane Noronha; Daúde, Matheus Martins; Ribeiro, Thales Henrique Cherubino; Gómez, Miguel Mauricio Díaz; Lima, André Almeida; Gomes, Luíz Antônio Augusto; Gomes, Marcos de Souza; Gandolfi, Peterson Elizandro; Amaral, Laurence Rodrigues do; Chalfun-Júnior, Antônio; Maluf, Wilson Roberto; Gomes, Matheus de Souza

doi:10.1038/s41598-018-34202-3

Cited by 24 publications

(12 citation statements)

References 250 publications

(288 reference statements)

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“…Solanum is by far the best characterized genus in the Solanaceae with regard to sRNA biology. Given that our predictions for this genus are similar to those from previous studies, we are likely approaching a consistent set of Solanum-specific miRNA predictions (Tomato Genome Consortium, 2012;Zhang et al, 2013;Cardoso et al, 2018;Zuo et al, 2020;Deng et al, 2021).…”

Section: Microrna Predictions Indicate An Expansion Of Novel Mirnas In Nicotiana Speciessupporting

confidence: 78%

The Evolutionary History of Small RNAs in the Solanaceae

Baldrich

Bélanger

Kong

et al. 2021

Preprint

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The Solanaceae or "nightshade" family is an economically important group that harbors a remarkable amount of diversity. To gain a better understanding of how the unique biology of the Solanaceae relates to the family's small RNA genomic landscape, we downloaded over 255 publicly available small RNA datasets that comprise over 2.6 billion reads of sequence data. We applied a suite of computational tools to predict and annotate two major small RNA classes: (1) microRNAs (miRNAs), typically 20-22 nt RNAs generated from a hairpin precursor and functioning in gene silencing, and (2) short interfering RNAs (siRNAs), including 24-nt heterochromatic siRNAs (hc-siRNAs) typically functioning to repress repetitive regions of the genome via RNA-directed DNA methylation, as well as secondary phased siRNAs (phasiRNAs) and trans-acting siRNAs (tasiRNAs) generated via miRNA-directed cleavage of a Pol II-derived RNA precursor. Our analyses described thousands of small RNA loci, including poorly-understood clusters of 22-nt siRNAs that accumulate during viral infection. The birth, death, expansion, and contraction of these small RNA loci are dynamic evolutionary processes that characterize the Solanaceae family. These analyses indicate that individuals within the same genus share similar small RNA landscapes, whereas comparisons between distinct genera within the Solanaceae reveal relatively few commonalities.

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Section: Microrna Predictions Indicate An Expansion Of Novel Mirnas In Nicotiana Speciessupporting

confidence: 78%

The Evolutionary History of Small RNAs in the Solanaceae

Baldrich

Bélanger

Kong

et al. 2021

Preprint

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“…miRNAs can be classified as conserved miRNAs or non-conserved miRNAs. Many miRNAs have been characterized in plants and play important roles in various signaling pathways [ 56 ]. For example, the target gene of miR156 is SPL , whose function is regulating development; the functions of miR159/ MYB are signaling pathways and development; and miR172/ AP2 functions in signaling pathways, flower development, stress responses, etc.…”

Section: Discussionmentioning

confidence: 99%

Comparative Transcriptome and sRNAome Analyses Reveal the Regulatory Mechanisms of Fruit Ripening in a Spontaneous Early-Ripening Navel Orange Mutant and Its Wild Type

et al. 2022

Genes

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A complex molecular regulatory network plays an important role in the development and ripening of fruits and leads to significant differences in apparent characteristics. Comparative transcriptome and sRNAome analyses were performed to reveal the regulatory mechanisms of fruit ripening in a spontaneous early-ripening navel orange mutant (‘Ganqi 4’, Citrus sinensis L. Osbeck) and its wild type (‘Newhall’ navel orange) in this study. At the transcript level, a total of 10792 genes were found to be differentially expressed between MT and WT at the four fruit development stages by RNA-Seq. Additionally, a total of 441 differentially expressed miRNAs were found in the four periods, and some of them belong to 15 families. An integrative analysis of the transcriptome and sRNAome data revealed some factors that regulate the mechanisms of formation of early-ripening traits. First, secondary metabolic materials, especially endogenous hormones, carotenoids, cellulose and pectin, obviously changed during fruit ripening in MT and WT. Second, we found a large number of differentially expressed genes (PP2C, SnRK, JAZ, ARF, PG, and PE) involved in plant hormone signal transduction and starch and sucrose metabolism, which suggests the importance of these metabolic pathways during fruit ripening. Third, the expression patterns of several key miRNAs and their target genes during citrus fruit development and ripening stages were examined. csi-miR156, csi-miR160, csi-miR397, csi-miR3954, and miRN106 suppressed specific transcription factors (SPLs, ARFs, NACs, LACs, and TCPs) that are thought to be important regulators involved in citrus fruit development and ripening. In the present study, we analyzed ripening-related regulatory factors from multiple perspectives and provide new insights into the molecular mechanisms that operate in the early-ripening navel orange mutant ‘Ganqi 4’.

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“…The studies based on specific characteristics of mature and precursor miR-NAs have been used in sequence groups in different species, from Protista to Metazoa and Plantae. (11,46,47,48) Our analyses using the libraries of small RNAs from male and female adult worms showed a validation of all 149 mature miRNAs found in the genome of S. haematobium Egypt [Supplementary data II (Table V)]. Some conserved miRNAs such as bantam-3p, let-7-3p, miR-124-3p and miR-10-5p demonstrated a large number of reads in two libraries studied, corroborating with the results found in a previously published study, (32) however, our findings refer to mature miRNAs.…”

Section: Discussionmentioning

confidence: 99%

Computational prediction and characterisation of miRNAs and their pathway genes in human schistosomiasis caused by Schistosoma haematobium

Cardoso

Araújo

Portilho

et al. 2020

Mem. Inst. Oswaldo Cruz

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BACKGROUND Key genes control the infectivity of the Schistosoma haematobium causing schistosomiasis. A method for understanding the regulation of these genes might help in developing new disease strategies to control schistosomiasis, such as the silencing mediated by microRNAs (miRNAs). The miRNAs have been studied in schistosome species and they play important roles in the post-transcriptional regulation of genes, and in parasite-host interactions. However, genome-wide identification and characterisation of novel miRNAs and their pathway genes and their gene expression have not been explored deeply in the genome and transcriptome of S. haematobium.OBJECTIVES Identify and characterise mature and precursor miRNAs and their pathway genes in the S. haematobium genome.METHODS Computational prediction and characterisation of miRNAs and genes involved in miRNA pathway from S. haematobium genome on SchistoDB. Conserved domain analysis was performed using PFAM and CDD databases. A robust algorithm was applied to identify mature miRNAs and their precursors. The characterisation of the precursor miRNAs was performed using RNAfold, RNAalifold and Perl scripts. FINDINGS We identified and characterised 14 putative proteins involved in miRNA pathway including ARGONAUTE and DICER in S. haematobium. Besides that, 149 mature miRNAs and 131 precursor miRNAs were identified in the genome including novel miRNAs. MAIN CONCLUSIONS miRNA pathway occurs in the S. haematobium, including endogenous miRNAs and miRNA pathway components, suggesting a role of this type of non-coding RNAs in gene regulation in the parasite. The results found in this work will open up a new avenue for studying miRNAs in the S. haematobium biology in helping to understand the mechanism of gene silencing in the human parasite Schistosome.

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New insights into tomato microRNAs

Cited by 24 publications

References 250 publications

The Evolutionary History of Small RNAs in the Solanaceae

The Evolutionary History of Small RNAs in the Solanaceae

Comparative Transcriptome and sRNAome Analyses Reveal the Regulatory Mechanisms of Fruit Ripening in a Spontaneous Early-Ripening Navel Orange Mutant and Its Wild Type

Computational prediction and characterisation of miRNAs and their pathway genes in human schistosomiasis caused by Schistosoma haematobium

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