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 October 2026 | Viewed by 1408

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 (2 papers)

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Research

19 pages, 6107 KB  
Article
Identification, Transcriptome, and Proteome Analysis of Expansin-like Subfamilies in the Storage Root Across I. trifida (2x), Wild (4x, 6x) and Cultivated Sweet Potatoes
by Jingjing Li, Zhiyu Zhang, Qiuzhuo Li, Chunli Geng, Haoxi Huang, Xiaojian Qin, Yongshu Liang, Wenbin Nan, Hanma Zhang, Yufan Fu and Ming Li
Plants 2026, 15(2), 305; https://doi.org/10.3390/plants15020305 - 20 Jan 2026
Viewed by 129
Abstract
The expansin-like subfamilies (EXLA and EXLB) are vital for plant cell wall dynamics, but it remains uncharacterized in wild tetraploid and hexaploid Ipomoea batatas, and its role in the storage root (SR) development is poorly understood. In this work, we identified 4, [...] Read more.
The expansin-like subfamilies (EXLA and EXLB) are vital for plant cell wall dynamics, but it remains uncharacterized in wild tetraploid and hexaploid Ipomoea batatas, and its role in the storage root (SR) development is poorly understood. In this work, we identified 4, 3, 3, and 3 EXLAs, alongside 11, 9, 13, and 8 EXLBs, in diploid I. trifida strain Y22, wild tetraploid I. batatas strain Y428B, and hexaploid I. batatas strain Y601, and cultivated sweet potato ‘Nancy Hall’, respectively. A comprehensive bioinformatic analysis of the expansin-like genes and proteins was performed to reveal their potential roles in SR development. Gene expression profiling showed that EXLA members were expressed during SR development, while approximately half of the EXLB members were expressed in Y22, Y428B (pencil root), Y601, and NH, respectively. Proteomic analysis (4D-DIA) detected 2, 1, 1, and 1 EXLAs, and 3, 3, 3, and 3 EXLBs in the mature SRs of the respective species. Integrated transcriptomic and proteomic analyses suggested that downregulating Iba6xEXLB2 and Iba6xEXLB1 may be associated with SR swelling in sweet potato. Furthermore, subcellular localization assays confirmed that Iba6xEXLB2 and Iba6xEXLB8 are localized to the cell wall/membrane. This study enhances the understanding of the expansin-like gene subfamily in sweet potato and its wild relatives and lays the groundwork for future functional studies on the role of expansin-like genes in SR development. Full article
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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 954
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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