Transcriptome Analysis and Gene Regulation in Plant Growth Development, 3rd Edition

A special issue of Plants (ISSN 2223-7747). This special issue belongs to the section "Plant Molecular Biology".

Deadline for manuscript submissions: 31 January 2026 | Viewed by 734

Special Issue Editors

College of Forestry and Biotechnology, Zhejiang Agriculture and Forestry University, Hangzhou 311300, China
Interests: photosynthesis; signal transduction; gene regulation; flower development
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Guest Editor
College of Advanced Agricultural Sciences, Zhejiang Agriculture and Forestry University, Hangzhou 311300, China
Interests: molecular breeding; gene regulation; plant genetics and genomics
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Guest Editor
College of Forestry and Biotechnology, Zhejiang Agriculture and Forestry University, Hangzhou, China
Interests: research on the molecular mechanism of wood formation and genetic engineering breeding of trees

Special Issue Information

Dear Colleagues,

Transcriptome sequencing has become more and more important for understanding biological phenomena, and provides vital insight for understanding gene regulatory mechanisms in the process of plant growth development. Therefore, it is a hot topic for many plant biologists, showing how to efficiently explore the information underlying transcriptome sequencing to understand the gene regulatory mechanisms of the phenomenon. In addition, an integrated multi-omics framework based on transcriptome analysis has provided insight into the gene regulatory mechanisms of plant growth development, especially in some non-model plants. The importance of new mathematical and statistical methods for transcriptome analysis will also help us to better understand the hidden secrets of plant growth and development. This Special Issue of Plants will highlight the new tools, methods, strategies, and perspectives of transcriptome analysis, and their role in explaining gene regulatory networks.

Dr. Yi He
Prof. Dr. Dali Zeng
Dr. Lichao Huang
Guest Editors

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Keywords

  • plant growth
  • plant development
  • transcriptome/genome analysis
  • genetics
  • gene expression
  • transcriptome
  • signal transduction
  • plant genome
  • transcriptome
  • proteome
  • gene expression
  • epigenetic regulations

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Published Papers (1 paper)

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Research

16 pages, 1406 KB  
Article
Transcriptional Regulation of the Phenylalanine Ammonia-Lyase (PAL) Gene Family in Mulberry Under Chitosan-Induced Stress
by Apidet Rakpenthai, Mutsumi Watanabe, Arunee Wongkaew and Sutkhet Nakasathien
Plants 2025, 14(17), 2783; https://doi.org/10.3390/plants14172783 - 5 Sep 2025
Viewed by 544
Abstract
Regulation of the phenylpropanoid pathway is critical for plant development and defense. This research investigates the transcriptional control of six Phenylalanine Ammonia-Lyase (PAL) gene homologs identified in the mulberry genome. A comprehensive in silico pipeline was employed to analyze the promoter [...] Read more.
Regulation of the phenylpropanoid pathway is critical for plant development and defense. This research investigates the transcriptional control of six Phenylalanine Ammonia-Lyase (PAL) gene homologs identified in the mulberry genome. A comprehensive in silico pipeline was employed to analyze the promoter architecture of these genes. Using the MEME suite, we identified three statistically significant conserved motifs within the 2000 bp upstream region. Subsequent TF binding prediction with FootprintDB for these motifs implicated the TCP, NAC, AP2/ERF, B3, and BBR-BPC families as potential regulators. A parallel analysis with PlantRegMap highlighted a high density of binding sites for the BBR-BPC and AP2/ERF families in the core promoter regions. A comparative analysis showed a weak correlation between the databases, underscoring the necessity of a multi-faceted predictive approach. Transcriptomic profiling under chitosan-induced conditions validated our in silico framework, suggesting the involvement of these TF families. Specifically, the data support NAC083 as a putative transcriptional activator and suggest a repressive function for members of the AP2/ERF and BBR-BPC families, providing a robust, experimentally supported model of PAL regulation. Full article
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