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Plant Genome Evolution and Environmental Adaptation
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Plant Genome Evolution and Environmental Adaptation

A special issue of International Journal of Molecular Sciences (ISSN 1422-0067). This special issue belongs to the section "Molecular Plant Sciences".

Deadline for manuscript submissions: closed (31 December 2025) | Viewed by 4695

Special Issue Editor

Prof. Dr. Zhonghu Li

E-Mail Website
Guest Editor
Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, College of Life Sciences, Northwest University, Xi’an, China
Interests: plant population genomics; molecular evolution; population genetics; evolutionary ecology
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

Plant genome evolution is very important to the species environmental adaptation. In general, plants are located in the special ecological environments, thay have always occurred the adaptive evolution to the various ecological geographic environments. This special issue aims to reveal the patterns and rules of plant genome evolution (including, bur not limitted to chloroplast genomics, mitochondrial genomics and nuclear genomics) and environmental adaptation in various ecosystems. The authors could also determine the evolutionary responses of some key family genes (for example, responses to the biotic and/or abiotic stresses) of plants in various environments. The issue will provide the novel insights into the understanding of plant genome evolution and environmental adaptation mechanisms.

Prof. Dr. Zhonghu Li
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 250 words) can be sent to the Editorial Office for assessment.

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. International Journal of Molecular Sciences is an international peer-reviewed open access semimonthly journal published by MDPI.

Please visit the Instructions for Authors page before submitting a manuscript. There is an Article Processing Charge (APC) for publication in this open access journal. For details about the APC please see here. 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 phylogeny
  • genome evolution
  • molecular evolution of cytoplasmic genomes
  • species divergence

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Published Papers (3 papers)

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Research

20 pages, 2379 KB  
Article
Positive-Strand RNA Viruses Induce LTR Retrotransposon Transcription and Extrachromosomal Circular DNA Generation in Plants
by Pavel Merkulov, Anna Bolotina, Anastasia Vlasova, Anna Ivakhnenko, Alena Prokofeva, Danil Perevozchikov, Elizaveta Kamarauli, Alexander Soloviev and Ilya Kirov
Int. J. Mol. Sci. 2026, 27(1), 286; https://doi.org/10.3390/ijms27010286 - 26 Dec 2025
Cited by 2 | Viewed by 1348
Abstract
Mobile elements, particularly long terminal repeat retrotransposons (LTR-RTEs), are abundant and dynamic components of plant genomes. Although viral infections are known to transcriptionally activate retrotransposons, it remains unclear whether such virus-induced activation leads to their mobilization. To address this question, we examined LTR-RTE [...] Read more.
Mobile elements, particularly long terminal repeat retrotransposons (LTR-RTEs), are abundant and dynamic components of plant genomes. Although viral infections are known to transcriptionally activate retrotransposons, it remains unclear whether such virus-induced activation leads to their mobilization. To address this question, we examined LTR-RTE activation in Arabidopsis thaliana, Brassica napus, and Nicotiana benthamiana following infection with the RNA viruses Tobacco rattle virus (TRV), Potato virus X (PVX), and Tobacco ringspot virus (TRSV). Nanopore cDNA sequencing revealed virus-specific transcriptional responses, with PVX uniquely triggering a strong transcriptional burst of diverse LTR-RTE families in N. benthamiana. To test the role of viral suppressors of RNA silencing (VSRs) in this process, we analyzed extrachromosomal circular DNA (eccDNA) from plants infected with TRV expressing the VSR P19. This analysis identified eccDNA derived from Ty3/Gypsy Galadriel elements, demonstrating that viral infection can promote not only retrotransposon transcription but also eccDNA production, which may indicate the ability of LTR-RTEs to transpose. These findings clearly illustrate that plant–virus interactions can induce not only changes in gene transcription, but also the activation of multiple retrotransposons, highlighting a potential evolutionary interface linking antiviral defense and transposon regulation. Full article
(This article belongs to the Special Issue Plant Genome Evolution and Environmental Adaptation)
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20 pages, 3604 KB  
Article
Dynamic Genetic Changes Reveal: Intra-Lineage Diversity, Not Admixture, Explains Amaranthus palmeri’s Success in China
by Jing-Jing Cao, Hong-Wei Wang, Jian-Guo Fu, Fang-Hao Wan, Jian-Ying Guo and Rui Wang
Int. J. Mol. Sci. 2025, 26(17), 8128; https://doi.org/10.3390/ijms26178128 - 22 Aug 2025
Cited by 1 | Viewed by 1556
Abstract
Global trade facilitates multiple introductions of alien species, yet the role of genetic admixture between divergent lineages in driving invasion success remains debated. Here, we address this question by analyzing dynamic genetic changes across invasion stages in the dioecious weed Amaranthus palmeri, [...] Read more.
Global trade facilitates multiple introductions of alien species, yet the role of genetic admixture between divergent lineages in driving invasion success remains debated. Here, we address this question by analyzing dynamic genetic changes across invasion stages in the dioecious weed Amaranthus palmeri, introduced to China from North and South America. Combining chloroplast phylogeography with nuclear genetic analyses, we systematically investigated genetic changes in populations at casual, naturalized, invasive, and dispersal stages. Initial casual populations originated from distinct North and South American lineages, but all established populations (naturalized, invasive, dispersal) retained only North American haplotypes. South American genetic introgression decreased progressively during invasion (from 34% in naturalized to 3% in dispersal populations), accompanied by declining inbreeding coefficients. Established populations exhibited high inter-population crosses within the North American lineage (54–60%), maintaining genetic diversity and overcoming bottlenecks. Our findings demonstrate that invasion success in A. palmeri may be driven by gene flow within the North American lineage, rather than admixture between divergent lineages. These findings enhance our understanding of the genetic mechanisms underpinning plant invasions, highlighting lineage-specific management as a critical strategy for controlling invasive populations. Full article
(This article belongs to the Special Issue Plant Genome Evolution and Environmental Adaptation)
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26 pages, 8704 KB  
Article
Genome-Wide Identification, Phylogeny, and Abiotic Stress Response Analysis of OSCA Family Genes in the Alpine Medicinal Herb Notopterygium franchetii
by Qi-Yue Zhang, Xiao-Jing He, Yan-Ze Xie, Li-Ping Zhou, Xin Meng, Jia Kang, Cai-Yun Luo, Yi-Nuo Wang, Zhong-Hu Li and Tian-Xia Guan
Int. J. Mol. Sci. 2025, 26(11), 5043; https://doi.org/10.3390/ijms26115043 - 23 May 2025
Cited by 2 | Viewed by 1338
Abstract
Hyperosmolality-gated calcium-permeable cation channel protein denoted as OSCA, which are mechanosensitive pore-forming ion channels, play a pivotal role in plants’ responses to abiotic stressors. Notopterygium franchetii, an endemic perennial plant species distributed in the Qinghai–Tibetan Plateau and its adjacent high-altitude regions, is [...] Read more.
Hyperosmolality-gated calcium-permeable cation channel protein denoted as OSCA, which are mechanosensitive pore-forming ion channels, play a pivotal role in plants’ responses to abiotic stressors. Notopterygium franchetii, an endemic perennial plant species distributed in the Qinghai–Tibetan Plateau and its adjacent high-altitude regions, is likely to have undergone adaptive evolution in response to extreme abiotic stress conditions. The current study was conducted to characterize the genome-wide characteristics and phylogenetic evolution of the OSCA gene family in N. franchetii and identify its response patterns to drought and high-temperature stresses. We examined the gene family’s structural features, phylogenetic relationships, and response to abiotic stresses. The N. franchetii genome had 29 OSCA gene family members on 11 chromosomes. Subcellular localization showed they were mainly in the cell membrane, and a promoter cis-acting element study found that the OSCA gene family contained methyl jasmonate, abscisic acid, and various adversity and hormone response components. Under drought stress, most of the NofOSCAs genes showed a tendency to increase over time in the roots of N. franchetii, while in the aboveground parts, most of the NofOSCAs genes showed a tendency to increase and then decrease. The expression of different NofOSCAs genes in N. franchetii also showed alternating changes under high-temperature stress. Nine members of NofOSCAs were found to be linked to the PPI network, and these members were involved in membrane structure, transmembrane transport, and ion channel function. Our analysis of differential expression revealed that the expression of OSCA genes differed among the different N. franchetii tissues, with the roots exhibiting the highest average expression level, and many genes displayed tissue-specific high expression patterns. These results provided novel insights into the phylogenetic evolution and abiotic stress response mechanisms in the high-altitude medicinal herb N. franchetii. Full article
(This article belongs to the Special Issue Plant Genome Evolution and Environmental Adaptation)
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