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Molecular Adaptation and Evolutionary Genetics in Plants
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Molecular Adaptation and Evolutionary Genetics 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: 24 November 2025 | Viewed by 1729

Special Issue Editor

Prof. Dr. Wei Zhang

E-Mail Website
Guest Editor
Marine College, Shandong University, Weihai 264209 China
Interests: plant systematics; molecular evolution; comparative genomics; bioinformatics

Special Issue Information

Dear Colleagues,

Adaptation and evolution have long captivated scientists, since the time of Charles Darwin. Over two centuries later, these topics continue to inspire rigorous inquiry within the scientific community. Recent advances in sequencing technologies have made it easier and more affordable to obtain genes and genomes, enhancing our understanding of evolution and adaptation at the molecular level. In this context, the Special Issue of Genes, entitled "Molecular Adaptation and Evolutionary Genetics in Plants", seeks to explore the intricate evolutionary mechanisms governing economically significant and evolutionarily important plants. By examining chloroplast, mitochondrial, and nuclear genomes, this Issue will provide a comprehensive perspective on plant evolution. The integration of microevolution, phylogeography, trait evolution, and species evolution will facilitate a thorough exploration of the factors shaping key plant characteristics. Ultimately, this Special Issue aims to illuminate the complex processes and driving forces influencing plant adaptation and evolution, offering valuable insights for scientific research and practical applications in agriculture and conservation.

If you are interested in contributing to this Special Issue, please let us know at your earliest convenience. We look forward to your reply.

Prof. Dr. Wei Zhang
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

  • molecular evolution
  • plastid genome
  • mitochondrial genome
  • nuclear genome
  • gene family

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Published Papers (2 papers)

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Research

20 pages, 6805 KiB  
Article
Genome-Wide Identification of the Polygalacturonase Gene Family and Its Potential Association with Abscission Zone in Capsicum annuum L.
by Lei He, Chen Lu, Xi Yan, Sha Yang, Peng Zhou, Wei Lai and Jianwen He
Genes 2025, 16(5), 579; https://doi.org/10.3390/genes16050579 - 14 May 2025
Viewed by 297
Abstract
Background: Polygalacturonase (PG) genes regulate plant organ abscission by degrading pectin in the cell wall. However, their association with pedicel abscission susceptibility in pepper remains poorly understood. Methods: 47 CaPG genes were identified were identified in the ‘Zunla1’ genome and characterized [...] Read more.
Background: Polygalacturonase (PG) genes regulate plant organ abscission by degrading pectin in the cell wall. However, their association with pedicel abscission susceptibility in pepper remains poorly understood. Methods: 47 CaPG genes were identified were identified in the ‘Zunla1’ genome and characterized by structural, evolutionary, and comparative genomic analyses. Their expression profiles across various tissues and fruit development stages were examined using transcriptome data. Ethephon treatment and qRT-PCR were employed to assess gene responses during ethylene-induced pedicel abscission. Results: The 47 CaPG genes were distributed across 12 chromosomes, with CaPG1 to CaPG5 unanchored. Most proteins were hydrophilic, nuclear-localized, and had promoters enriched in light-responsive elements. Collinearity analysis revealed limited segmental duplication, and Ka/Ks values indicated strong purifying selection. Phylogenetic and collinearity analyses showed that CaPG genes are more closely related to those in tomato than in Arabidopsis or maize. Expression profiling revealed tissue- and stage-specific patterns, with 21 CaPG genes associated with pedicel abscission susceptibility. Ethephon treatment enhanced abscission and upregulated several CaPG genes. Conclusions: This study offers insights into the CaPG gene family’s structure, evolution, and function. Specific CaPG genes likely contribute to ethylene-mediated pedicel abscission, providing potential targets for improving fruit-retention traits in pepper. Full article
(This article belongs to the Special Issue Molecular Adaptation and Evolutionary Genetics in Plants)
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16 pages, 5136 KiB  
Article
Analysis of the Codon Usage Bias Pattern in the Chloroplast Genomes of Chloranthus Species (Chloranthaceae)
by Jisi Zhang and Miao Feng
Genes 2025, 16(2), 186; https://doi.org/10.3390/genes16020186 - 2 Feb 2025
Cited by 1 | Viewed by 1029
Abstract
Background: The codon preference of chloroplast genomes not only reflects mutation patterns during the evolutionary processes of species but also significantly affects the efficiency of gene expression. This characteristic holds significant scientific importance in the application of chloroplast genetic engineering and the genetic [...] Read more.
Background: The codon preference of chloroplast genomes not only reflects mutation patterns during the evolutionary processes of species but also significantly affects the efficiency of gene expression. This characteristic holds significant scientific importance in the application of chloroplast genetic engineering and the genetic improvement of species. Chloranthus, an ancestral angiosperm with significant economic, medicinal, and ornamental value, belongs to the basal angiosperms. However, the codon usage patterns among Chloranthus species have remained unclear. Methods: To investigate codon usage bias and its influencing factors in Chloranthus chloroplast genomes, we utilized CodonW, CUSP, and SPSS software to analyze the chloroplast genomes of seven Chloranthus species. Results: In this study, we reported and characterized the complete chloroplast genome of the Chinese endemic species Chloranthus angustifolius. The phylogenetic tree based on the whole chloroplast genomes showed that C. angustifolius is sister to Chloranthus fortunei, and the genus Chloranthus is divided into two major clades, consistent with previous studies. Our results revealed that the GC content at different codon positions across all seven Chloranthus species was less than 50%, with GC1 > GC2 > GC3. Additionally, the average effective number of codons (ENC) values exceeded 45. A total of 10 shared optimal codons were identified, nine of which end with A or U. PR2-plot, ENC-plot, and neutrality plot analyses indicated that natural selection primarily influenced codon usage bias in the chloroplast genomes of Chloranthus. Conclusions: We newly obtained the chloroplast genome of C. angustifolius and proposed that natural selection played a key role in codon usage patterns in Chloranthus species. These findings contribute to our understanding of evolutionary history and genetic diversity within this genus. Full article
(This article belongs to the Special Issue Molecular Adaptation and Evolutionary Genetics in Plants)
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