In silico Characterisation and Phylogenetic Analysis of Two Evolutionarily Conserved miRNAs (miR166 and miR171) from Black Pepper (Piper nigrum L.)

Asha, S; Joy, Nisha; Soniya, E. V.

doi:10.1007/s11105-012-0532-5

Cited by 17 publications

(13 citation statements)

References 77 publications

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“…The read counts of known miRNAs varied from 0 to 4,659,812. miR166 family was largely enriched in both sequencing datasets. As reported previously, miR166 family was also abundant in other plant species, i.e., Arabidopsis, black pepper (Zhu et al, 2011; Asha et al, 2013). …”

Section: Resultssupporting

confidence: 70%

Identification of Submergence-Responsive MicroRNAs and Their Targets Reveals Complex MiRNA-Mediated Regulatory Networks in Lotus (Nelumbo nucifera Gaertn)

Jin

Mattson

et al. 2017

Front. Plant Sci.

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MicroRNAs (miRNAs) are endogenous non-coding RNAs with important regulatory functions in plant development and stress responses. However, their population abundance in lotus (Nelumbo nucifera Gaertn) has so far been poorly described, particularly in response to stresses. In this work, submergence-related miRNAs and their target genes were systematically identified, compared, and validated at the transcriptome-wide level using high-throughput sequencing data of small RNA, Mrna, and the degradome. A total of 128 known and 20 novel miRNAs were differentially expressed upon submergence. We identified 629 target transcripts for these submergence-responsive miRNAs. Based on the miRNA expression profiles and GO and KEGG annotation of miRNA target genes, we suggest possible molecular responses and physiological changes of lotus in response to submergence. Several metabolic, physiological and morphological adaptations-related miRNAs, i.e., NNU_far-miR159, NNU_gma-miR393h, and NNU_aly-miR319c-3p, were found to play important regulatory roles in lotus response to submergence. This work will contribute to a better understanding of miRNA-regulated adaption responses of lotus to submergence stress.

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Section: Resultssupporting

confidence: 70%

Identification of Submergence-Responsive MicroRNAs and Their Targets Reveals Complex MiRNA-Mediated Regulatory Networks in Lotus (Nelumbo nucifera Gaertn)

Jin

Mattson

et al. 2017

Front. Plant Sci.

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“…Retrieved mature miRNAs of dicotyledons were allowed to homology search with 763 nonredundant ESTs of C. capsularis where 621 ESTs were identified for the further screening process. Non-coding ESTs were prioritized for being the putative miRNAs candidates [96,97,98] and only 36 non-coding ESTs were finalized in the present study. Different criteria were set up for screening the ESTs in order to identify the putative miRNAs of jute [99,100].…”

Section: Discussionmentioning

confidence: 99%

In silicoIdentification and Functional Characterization of Conserved miRNAs in Fibre Biogenesis CropCorchorus capsularis

Hasan

Ahmed

et al. 2020

Preprint

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Corchorus capsularis, commonly known as jute occupies the leading position in the production of natural fibre and fibre based products alongside lower environmental threat. Nowadays, the study of lignin biosynthesis pathways with other molecular basis of fibres formation are being more focused for its economic perspective. Small noncoding ~21 to 24 nt nucleotides long microRNAs play significant roles in regulating the gene expression as well as different functions in cellular growth and development. Here, the study adopted a comprehensive in silico approach to identify and characterize the conserved miRNAs in the genome of C. capsularis including specific gene targets involved in the crucial cellular process. Expressed Sequence Tags (ESTs) based homology search of 3350 known miRNAs of dicotyledons were allowed against 763 nonredundant ESTs of jute genome resulted in the prediction of 5 potential miRNA candidates belonging five different miRNA families (miR1536, miR9567-3p, miR4391, miR11300, and miR8689). The putative miRNAs were 18 nucleotide length, within a range of -0.49 to -1.56 MFEI values and 55% to 61% of (A+U) content of their correspondence pre-miRNAs. A total of 1052 gene targets of putative miRNAs were identified and their functions were extensively analyzed. Most of the gene targets were involved in plant growth, cell cycle regulation, organelle synthesis, developmental process and environmental responses. The five gene targets, namely, NAC Domain Containing Protein, WRKY DNA binding protein, 3-dehydroquinate synthase, Sadenosyl-L-Met-dependent methyl transferase and Vascular-related NAC-Domain were found to be involved in the lignin biosynthesis, phenylpropanoid pathways and secondary wall formation which could play significant roles in the overall fibre biogenesis. The characterization of conserved miRNAs and their functional annotation of specific gene targets might enhance the more miRNA discovery, strengthening the complete understanding of miRNAs association in the cellular basis of lignin biosynthesis towards the production of high standard jute products.

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“…Characterizing expression of miRNAs in different tissues may provide clues as to the sites of function of these miRNAs (Asha et al, 2013). To improve our understanding of the complex regulatory network in various tissues in peach, we used qPCR technology to track changes in miR166 expression, in the same three tissues at the same five development stages.…”

Section: Discussionmentioning

confidence: 99%

“…Since the discovery of the first miRNA in plants in (Park et al, 2002, thousands of miRNAs have been identified experimentally or computationally from a variety of species, such as beans (Arenas-Huertero et al, 2009), peanut (Zhao et al, 2010), maize (Jiao et al, 2011), and opium poppy (Unver et al, 2010). Many miRNA families are evolutionarily conserved across plant species, in which they are capable of regulating expression of protein-coding genes (Asha et al, 2013). Plant miRNAs are highly complementary to their targets, with no more than fournt mismatches (Bartel, 2004).…”

Section: Introductionmentioning

confidence: 99%

“…The conserved miR166 family is widely considered to have highly conserved targets that encode proteins of the class III homeodomainleucine zipper (HD-ZIP III) family in a broad range of plant species that includes olive (Donaire et al, 2011), citrus (Song et al, 2009), pepper (Asha et al, 2013), and cotton (Qiu et al, 2007). Members of the HD-ZIP III transcriptional factors are plant-specific and regulate critical aspects of plant development, including lateral organ polarity, apical and lateral meristem formation, and vascular development (Ruberti et al, 1991).…”

Section: Introductionmentioning

confidence: 99%

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Isolation and expression analysis of four HD-ZIP III family genes targeted by microRNA166 in peach

Zhang¹,

Zhang²,

J³

et al. 2015

Genet. Mol. Res.

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ABSTRACT. MicroRNA166 (miR166) is known to have highly conserved targets that encode proteins of the class III homeodomain-leucine zipper (HD-ZIP III) family, in a broad range of plant species. To further understand the relationship between HD-ZIP III genes and miR166, four HD-ZIP III family genes (PpHB14, PpHB15, PpHB8, and PpREV) were isolated from peach (Prunus persica) tissue and characterized. Spatio-temporal expression profiles of the genes were analyzed. Genes of the peach HD-ZIP III family were predicted to encode five conserved domains. Deduced amino acid sequences and tertiary structures of the four peach HD-ZIP III genes were highly conserved, with corresponding genes in Arabidopsis thaliana. The expression level of four targets displayed the opposite trend to that of miR166 throughout fruit development, with the exception of PpHB14 from 35 to 55 days after full bloom (DAFB). This finding indicates that miR166 may negatively regulate its four targets throughout fruit development. As for leaf and phloem, the same trend in expression level was observed between four targets and miR166 from 75 to 105 DAFB.

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In silico Characterisation and Phylogenetic Analysis of Two Evolutionarily Conserved miRNAs (miR166 and miR171) from Black Pepper (Piper nigrum L.)

Cited by 17 publications

References 77 publications

Identification of Submergence-Responsive MicroRNAs and Their Targets Reveals Complex MiRNA-Mediated Regulatory Networks in Lotus (Nelumbo nucifera Gaertn)

Identification of Submergence-Responsive MicroRNAs and Their Targets Reveals Complex MiRNA-Mediated Regulatory Networks in Lotus (Nelumbo nucifera Gaertn)

In silicoIdentification and Functional Characterization of Conserved miRNAs in Fibre Biogenesis CropCorchorus capsularis

Isolation and expression analysis of four HD-ZIP III family genes targeted by microRNA166 in peach

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