Non-coding RNA in Plants

A special issue of Genes (ISSN 2073-4425). This special issue belongs to the section "Plant Genetics and Genomics".

Deadline for manuscript submissions: closed (15 June 2022) | Viewed by 3150

Special Issue Editors


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Guest Editor
School of Life Sciences, East China Normal University, Shanghai 200241, China
Interests: non-coding RNAs; plant development; abiotic stress; plant molecular biology; microRNA

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Guest Editor
Guangdong Provincial Key Laboratory of Biotechnology for Plant Development, School of Life Science, South China Normal University, Guangzhou 510631, China
Interests: small RNAs; RNA silencing; epigenetic regulation; abiotic/biotic stress

Special Issue Information

Dear Colleagues,

In the past three decades, a remarkable number of non-coding RNAs (ncRNAs), such as microRNA (miRNA), small interfering RNA (siRNA), and lncRNA, have been identified in plants. ncRNAs are not only transcribed from intergenic regions, antisense strands of protein-coding gene regions, and pseudogenes, but also derived from the processing of mRNAs, rRNAs, and tRNAs, e.g., circRNAs, rRNA-derived siRNAs (risiRNAs), and tRNA-derived small RNAs (tsRNAs). Despite the lack of protein-coding potential, the importance of ncRNAs in the regulation of gene expression has been recognized. Many ncRNAs are largely involved in the transcriptional and post-transcriptional regulation of gene expression. ncRNAs have also been shown to play crucial roles in a variety of biological process, such as plant development, abiotic stress response, and plant–microbe interaction. With the progress of high-throughput sequencing technology and functional analysis, emerging evidence has revealed that the world of ncRNAs is continuously expanding. Although thousands of ncRNAs have been predicated or identified, their biological function still needs to be further dug out. Functional characterization of ncRNAs is a promising research endeavor to gain new insights into their biological roles. This issue focuses on novel function of ncRNAs in plants.

Dr. Jun Yan
Dr. Zhong-hui Zhang
Guest Editors

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Keywords

  • non-coding RNA (ncRNA)
  • miRNA
  • siRNA
  • long ncRNA
  • functional analysis
  • plants
  • plant development
  • abiotic stress
  • biotic stress
  • epigenetics

Published Papers (1 paper)

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Research

22 pages, 4243 KiB  
Article
Transcriptome Profiling Reveals Role of MicroRNAs and Their Targeted Genes during Adventitious Root Formation in Dark-Pretreated Micro-Shoot Cuttings of Tetraploid Robinia pseudoacacia L.
by Saleem Uddin, Muhammad Zeeshan Munir, Sadia Gull, Aamir Hamid Khan, Aimal Khan, Dilawar Khan, Muhammad Asif Khan, Yue Wu, Yuhan Sun and Yun Li
Genes 2022, 13(3), 441; https://doi.org/10.3390/genes13030441 - 27 Feb 2022
Cited by 6 | Viewed by 2753
Abstract
Tetraploid Robinia pseudoacacia L. is a difficult-to-root species, and is vegetatively propagated through stem cuttings. Limited information is available regarding the adventitious root (AR) formation of dark-pretreated micro-shoot cuttings. Moreover, the role of specific miRNAs and their targeted genes during dark-pretreated AR formation [...] Read more.
Tetraploid Robinia pseudoacacia L. is a difficult-to-root species, and is vegetatively propagated through stem cuttings. Limited information is available regarding the adventitious root (AR) formation of dark-pretreated micro-shoot cuttings. Moreover, the role of specific miRNAs and their targeted genes during dark-pretreated AR formation under in vitro conditions has never been revealed. The dark pretreatment has successfully promoted and stimulated adventitious rooting signaling-related genes in tissue-cultured stem cuttings with the application of auxin (0.2 mg L−1 IBA). Histological analysis was performed for AR formation at 0, 12, 36, 48, and 72 h after excision (HAE) of the cuttings. The first histological events were observed at 36 HAE in the dark-pretreated cuttings; however, no cellular activities were observed in the control cuttings. In addition, the present study aimed to uncover the role of differentially expressed (DE) microRNAs (miRNAs) and their targeted genes during adventitious root formation using the lower portion (1–1.5 cm) of tetraploid R. pseudoacacia L. micro-shoot cuttings. The samples were analyzed using Illumina high-throughput sequencing technology for the identification of miRNAs at the mentioned time points. Seven DE miRNA libraries were constructed and sequenced. The DE number of 81, 162, 153, 154, 41, 9, and 77 miRNAs were upregulated, whereas 67, 98, 84, 116, 19, 16, and 93 miRNAs were downregulated in the following comparisons of the libraries: 0-vs-12, 0-vs-36, 0-vs-48, 0-vs-72, 12-vs-36, 36-vs-48, and 48-vs-72, respectively. Furthermore, we depicted an association between ten miRNAs (novel-m0778-3p, miR6135e.2-5p, miR477-3p, miR4416c-5p, miR946d, miR398b, miR389a-3p, novel m0068-5p, novel-m0650-3p, and novel-m0560-3p) and important target genes (auxin response factor-3, gretchen hagen-9, scarecrow-like-1, squamosa promoter-binding protein-like-12, small auxin upregulated RNA-70, binding protein-9, vacuolar invertase-1, starch synthase-3, sucrose synthase-3, probable starch synthase-3, cell wall invertase-4, and trehalose phosphatase synthase-5), all of which play a role in plant hormone signaling and starch and sucrose metabolism pathways. The quantitative polymerase chain reaction (qRT-PCR) was used to validate the relative expression of these miRNAs and their targeted genes. These results provide novel insights and a foundation for further studies to elucidate the molecular factors and processes controlling AR formation in woody plants. Full article
(This article belongs to the Special Issue Non-coding RNA in Plants)
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