Identification of microRNAs and relative target genes in Moringa oleifera leaf and callus

Pirro, S.; Matić, Ivana Z.; Guidi, Arianna; Zanella, Letizia; Gismondi, Angelo; Cicconi, Rosella; Bernardini, Roberta; Colizzi, Vittorio; Canini, Antonella; Mattei, Maurizio; Galgani, Andrea

doi:10.1038/s41598-019-51100-4

Cited by 16 publications

(12 citation statements)

References 91 publications

(97 reference statements)

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“…In our previous studies 65 , 66 , we focused on the characterization of microRNAs from M. oleifera, a medicinal plant widely distributed in subtropical areas and popularly called the “miracle tree”. Although the anti-inflammatory and immunomodulatory properties of this plant have been widely studied and associated with polyphenols 67 , the role of microRNAs in this context has been underexplored.…”

Section: Resultsmentioning

confidence: 99%

“…Although the anti-inflammatory and immunomodulatory properties of this plant have been widely studied and associated with polyphenols 67 , the role of microRNAs in this context has been underexplored. In 2019, we identified a set of high-confidence (hc, 131), low-confidence (lc, 300) and novel (n, 302) microRNAs from the leaves, seeds and calli under normal and cold-stress conditions 66 .…”

Section: Resultsmentioning

confidence: 99%

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The microRNA analysis portal is a next-generation tool for exploring and analyzing miRNA-focused data in the literature

Pirro¹,

Matić

Colizzi

et al. 2021

Sci Rep

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MicroRNAs constitute a class of noncoding small RNAs involved in the posttranscriptional regulation of many biological pathways. In recent years, microRNAs have also been associated with regulation across kingdoms, demonstrating that exogenous miRNAs can function in mammals in a fashion similar to mammalian miRNAs. The growing interest in microRNAs and the increasing amount of literature and molecular and biomedical data available make it difficult to identify records of interest and keep up to date with novel findings. For these reasons, we developed the microRNA Analysis Portal (MAP). MAP selects relevant miRNA-focused articles from PubMed, links biomedical and molecular data and applies bioinformatics modules. At the time of this writing, MAP represents the richest, most complete and integrated database focused on microRNAs. MAP also integrates an updated version of MirCompare (2.0), a computational platform used for selecting plant microRNAs on the basis of their ability to regulate mammalian genes. Both MAP and MirCompare functionalities were used to predict that microRNAs from Moringa oleifera have putative roles across kingdoms by regulating human genes coding for proteins of the immune system. Starting from a selection of 94 human microRNAs, MirCompare selected 6 Moringa oleifera functional homologs. The subsequent prediction of human targets and areas of functional enrichment highlighted the central involvement of these genes in regulating immune system processes, particularly the host-virus interaction processes in hepatitis B, cytomegalovirus, papillomavirus and coronavirus. This case of use showed how MAP can help to perform complex queries without any computational background. MAP is available at http://stablab.uniroma2.it/MAP.

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Section: Resultsmentioning

confidence: 99%

Section: Resultsmentioning

confidence: 99%

The microRNA analysis portal is a next-generation tool for exploring and analyzing miRNA-focused data in the literature

Pirro¹,

Matić

Colizzi

et al. 2021

Sci Rep

Self Cite

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“…Like MIR397, MIR159 has been studied to regulate the development of callus in multiple plants, such as Dimocarpus longan ( Lin and Lai 2013 ; Xu et al. 2020 ), Moringa oleifera ( Pirro et al. 2019 ), and Larix leptolepis ( Zhang et al.…”

Section: Discussionmentioning

confidence: 99%

Genome-wide identification of microRNAs involved in the somatic embryogenesis of Eucalyptus

Qin

Zhang

et al. 2021

G3 Genes|Genomes|Genetics

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MicroRNAs (miRNAs) are small noncoding RNAs (18∼24 nt) and function in many biological processes in plants. Although Eucalyptus trees are widely planted across the world, our understanding of the miRNA regulation in the somatic embryogenesis (SE) of Eucalyptus is still poor. Here we reported, for the first time, the miRNA profiles of differentiated and dedifferentiated tissues of two Eucalyptus species and identified miRNAs involved in SE of Eucalyptus. Stem and tissue-culture induced callus were obtained from the subculture seedlings of E. camaldulensis and E. grandis x urophylla, and were used as differentiated and dedifferentiated samples, respectively. Small RNA sequencing generated 304.2 million clean reads for the Eucalyptus samples (n = 3) and identified 888 miRNA precursors (197 known and 691 novel) for Eucalyptus. These miRNAs were mainly distributed in chromosomes Chr03, Chr05 and Chr08, and can produce 46 miRNA clusters. Then, we identified 327 and 343 differentially expressed miRNAs (DEmiRs) in the dedifferentiation process of E. camaldulensis and E. grandis x urophylla, respectively. DEmiRs shared by the two Eucalyptus species might be involved in the development of embryonic callus, such as MIR156, MIR159, MIR160, MIR164, MIR166, MIR169, MIR171, MIR399 and MIR482. Notably, we identified 81 up-regulated and 67 down-regulated miRNAs specific to E. camaldulensis, which might be associated with the high embryogenic potential. Target prediction and functional analysis showed they might be involved in longevity regulating and plant hormone signal transduction pathways. Further, using the gene expression profiles we observed the negative regulation of miRNA∼target pairs, such as MIR160∼ARF18, MIR396∼GRF6, MIR166∼ATHB15/HD-ZIP and MIR156/MIR157∼SPL1. Interestingly, transcription factors such as WRKY, MYB, GAMYB, TCP4 and PIL1 were found to be regulated by the DEmiRs. The genes encoding PIL1 and RPS21C, regulated by up-regulated miRNAs (e.g., egd-N-miR63-5p, egd-N-miR63-5p and MIR169,) were down-regulated exclusively in the dedifferentiation of E. camaldulensis. This is the first time to study the miRNA regulation in the dedifferentiation process of Eucalyptus and it will provide a valuable resource for future studies. More importantly, it will improve our understanding of miRNA regulation during the somatic embryogenesis of Eucalyptus and benefit the Eucalyptus breeding program.

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“…Also, miR397b-3p was up-regulated in the callus of both E. camaldulensis and E. grandis x urophylla, and miR397a-3p was up-regulated only in the dedifferentiated tissue of E. camaldulensis (Additional le 3). Like MIR397, MIR159 has been studied to regulate the development of callus in multiple plants, such as Dimocarpus longan [21,22], Moringa oleifera [23] and Larix leptolepis [24]. miR159 has been shown to be induced by ABA and to regulate MYB33 during the seed germination of Arabidopsis [25].…”

Section: Discussionmentioning

confidence: 99%

Genome-Wide Identification of MicroRNAs Associated With the Somatic Embryogenesis in Eucalyptus

Qin

Zhang

et al. 2020

Preprint

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Background: MicroRNAs (miRNAs) are a class of small noncoding RNAs with 18-24 nucleotides in length and function in many biological processes in plant. Although Eucalyptus trees are widely planted across the world, our understanding of the miRNA regulation in the somatic embryogenesis of Eucalyptus is still poor. Here we reported for the first time the miRNA profiles of differentiated and dedifferentiated tissues of two Eucalyptus cultivars and identified miRNAs involved in the somatic embryogenesis of Eucalyptus.Results: Stem and tissue-culture induced callus were obtained from the subculture seedlings of E. camaldulensis and E. grandis x urophylla, and were used as differentiated and dedifferentiated samples, respectively. We generated 346.4 million reads for 12 samples (n=3) and identified 888 miRNA precursors (197 known and 691 novel) which can produce 1,067 mature miRNAs. These miRNAs were mainly distributed in chromosomes Chr03, Chr05 and Chr08, and can produce 46 miRNA clusters. In these samples we detected 998 miRNAs with TPM (transcripts per million reads) > 5 and found that highly expressed miRNAs varied across samples. We identified 327 and 343 differentially expressed miRNAs in the dedifferentiation process of E. camaldulensis and E. grandis x urophylla, respectively. Dysregulated miRNAs shared by the two cultivars might be involved in the development of embryonic callus of Eucalyptus, such as MIR156, MIR159, MIR160, MIR164, MIR166, MIR169, MIR171, MIR399 and MIR482. We also identified 81 up-regulated (e.g., miR159c-3p, miR167a-5p, miR397a-3p, miR397c-5p, miR397d-3p, miR397d-5p, N-miR1-5p and N-miR5-5p) and 67 down-regulated (e.g., miR482b-3p, N-miR3-3p, miR156a-3p, N-miR40-3p and N-miR18-5p) miRNAs specific to E. camaldulensis. Target prediction and functional analysis showed they might be involved in longevity regulating and plant hormone signal transduction pathways. Then, the expression patterns of these miRNAs were confirmed by qRT-PCR. Conclusions: This is the first time to study the miRNAs profiles in the dedifferentiation process of Eucalyptus and it will provide a valuable resource for future studies. More importantly, our findings will improve our understanding of miRNA regulation and molecular mechanisms during the somatic embryogenesis of Eucalyptus, and the output of this study will benefit the Eucalyptus breeding program.

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Identification of microRNAs and relative target genes in Moringa oleifera leaf and callus

Cited by 16 publications

References 91 publications

The microRNA analysis portal is a next-generation tool for exploring and analyzing miRNA-focused data in the literature

The microRNA analysis portal is a next-generation tool for exploring and analyzing miRNA-focused data in the literature

Genome-wide identification of microRNAs involved in the somatic embryogenesis of Eucalyptus

Genome-Wide Identification of MicroRNAs Associated With the Somatic Embryogenesis in Eucalyptus

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