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Advances in Genetics and Genomics of Plants: 2nd Edition
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Advances in Genetics and Genomics of Plants: 2nd Edition

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

Deadline for manuscript submissions: 25 February 2025 | Viewed by 1634

Special Issue Editor

Dr. Mingcheng Wang

E-Mail Website
Guest Editor
Institute for Advanced Study, Chengdu University, Chengdu 610106, China
Interests: plant genomics; comparative genomic analysis; functional gene analysis
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

Following the recent advances in molecular genetics and high-throughput sequencing technologies, continuous and rapid progress has revealed the complex and varied genomic characteristics and genetics of plants. In the recent past, diverse omics technologies such as genomics, transcriptomics, epigenomics, proteomics, and metabolomics have developed rapidly, providing powerful tools for the comprehensive study of plant nuclear, mitochondrial, and chloroplast genomes and their dynamics. These studies provide valuable insights into the underlying genetic mechanisms driving the complex traits of plants, helping us transform and use plant resources more efficiently. In this Special Issue, we aim to focus on the applications of cutting-edge technologies in the genetic and genomic study of plant species that are related to scientific questions of wide concern. Studies including high-throughput sequencing data analysis and experimental validation analysis on nuclear and organelle genomes are welcome. Both theoretical and empirical contributions will be considered.

Dr. Mingcheng Wang
Guest Editor

Manuscript Submission Information

Manuscripts should be submitted online at www.mdpi.com by registering and logging in to this website. Once you are registered, click here to go to the submission form. Manuscripts can be submitted until the deadline. All submissions that pass pre-check are peer-reviewed. Accepted papers will be published continuously in the journal (as soon as accepted) and will be listed together on the special issue website. Research articles, review articles as well as short communications are invited. For planned papers, a title and short abstract (about 100 words) can be sent to the Editorial Office for announcement on this website.

Submitted manuscripts should not have been published previously, nor be under consideration for publication elsewhere (except conference proceedings papers). All manuscripts are thoroughly refereed through a single-blind peer-review process. A guide for authors and other relevant information for submission of manuscripts is available on the Instructions for Authors page. Genes is an international peer-reviewed open access monthly journal published by MDPI.

Please visit the Instructions for Authors page before submitting a manuscript. The Article Processing Charge (APC) for publication in this open access journal is 2600 CHF (Swiss Francs). Submitted papers should be well formatted and use good English. Authors may use MDPI's English editing service prior to publication or during author revisions.

Keywords

  • plant genomics
  • plant genetics
  • high-throughput sequencing
  • genome dynamics
  • organelle genome
  • experimental validation

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Published Papers (2 papers)

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Research

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17 pages, 3928 KiB  
Article
Dynamic Chromatin Accessibility and Gene Expression Regulation During Maize Leaf Development
by Yiduo Wang, Shuai Wang, Yufeng Wu, Jiawen Cheng and Haiyan Wang
Genes 2024, 15(12), 1630; https://doi.org/10.3390/genes15121630 - 20 Dec 2024
Viewed by 607
Abstract
Background/Objectives: Chromatin accessibility is closely associated with transcriptional regulation during maize (Zea mays) leaf development. However, its precise role in controlling gene expression at different developmental stages remains poorly understood. This study aimed to investigate the dynamics of chromatin accessibility and [...] Read more.
Background/Objectives: Chromatin accessibility is closely associated with transcriptional regulation during maize (Zea mays) leaf development. However, its precise role in controlling gene expression at different developmental stages remains poorly understood. This study aimed to investigate the dynamics of chromatin accessibility and its influence on genome-wide gene expression during the BBCH_11, BBCH_13, and BBCH_17 stages of maize leaf development. Methods: Maize leaves were collected at the BBCH_11, BBCH_13, and BBCH_17 developmental stages, and chromatin accessibility was assessed using ATAC-seq. RNA-seq was performed to profile gene expression. Integrated analysis of ATAC-seq and RNA-seq data was conducted to elucidate the relationship between chromatin accessibility and transcriptional regulation. Results: A total of 46,808, 38,242, and 41,084 accessible chromatin regions (ACRs) were identified at the BBCH_11, BBCH_13, and BBCH_17 stages, respectively, with 23.4%, 12.2%, and 21.9% of these regions located near transcription start sites (TSSs). Integrated analyses revealed that both the number and intensity of ACRs significantly influence gene expression levels. Motif analysis identified key transcription factors associated with leaf development and potential transcriptional repressors among genes, showing divergent regulation patterns in ATAC-seq and RNA-seq datasets. Conclusions: These findings demonstrate that chromatin accessibility plays a crucial role in regulating the spatial and temporal expression of key genes during maize leaf development by modulating transcription factor binding. This study provides novel insights into the regulatory mechanisms underlying maize leaf development, contributing to a deeper understanding of chromatin-mediated gene expression. Full article
(This article belongs to the Special Issue Advances in Genetics and Genomics of Plants: 2nd Edition)
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Review

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18 pages, 2505 KiB  
Review
From Species to Varieties: How Modern Sequencing Technologies Are Shaping Medicinal Plant Identification
by Mingcheng Wang, Haifeng Lin, Hongqiang Lin, Panyue Du and Shuqiao Zhang
Genes 2025, 16(1), 16; https://doi.org/10.3390/genes16010016 - 26 Dec 2024
Viewed by 613
Abstract
Background/Objectives: Modern sequencing technologies have transformed the identification of medicinal plant species and varieties, overcoming the limitations of traditional morphological and chemical approaches. This review explores the key DNA-based techniques, including molecular markers, DNA barcoding, and high-throughput sequencing, and their contributions to enhancing [...] Read more.
Background/Objectives: Modern sequencing technologies have transformed the identification of medicinal plant species and varieties, overcoming the limitations of traditional morphological and chemical approaches. This review explores the key DNA-based techniques, including molecular markers, DNA barcoding, and high-throughput sequencing, and their contributions to enhancing the accuracy and reliability of plant identification. Additionally, the integration of multi-omics approaches is examined to provide a comprehensive understanding of medicinal plant identity. Methods: The literature search for this review was conducted across databases such as Google Scholar, Web of Science, and PubMed, using keywords related to plant taxonomy, genomics, and biotechnology. Inclusion criteria focused on peer-reviewed studies closely related to plant identification methods and techniques that contribute significantly to the field. Results: The review highlights that while sequencing technologies offer substantial improvements, challenges such as high costs, technical expertise, and the lack of standardized protocols remain barriers to widespread adoption. Potential solutions, including AI-driven data analysis and portable sequencers, are discussed. Conclusions: This review provides a comprehensive overview of molecular techniques, their transformative impact, and future perspectives for more accurate and efficient medicinal plant identification. Full article
(This article belongs to the Special Issue Advances in Genetics and Genomics of Plants: 2nd Edition)
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