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Power Up Plant Genetic Research with Genomic Data: 3rd Edition

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

Deadline for manuscript submissions: 20 December 2025 | Viewed by 2002

Special Issue Editors


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Guest Editor

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Guest Editor
Lab of Plant Genetics and Genomics, Kazusa DNA Research Institute, Kisarazu, Chiba 292-0818, Japan
Interests: molecular genetics; breeding, whole genome sequencing; digital phenotyping
Special Issues, Collections and Topics in MDPI journals
Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, CT 06511, USA
Interests: genome; domestication; quantitative trait loci; growth and development; agriculture; Arabidopsis; soybean
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

Developments in plant genetics and genomics research often lag behind those in mammals and humans, largely due to the complexity of plant genomes and limitations in research resources. However, with advances in sequencing technologies, building high-quality genomes and sequencing large plant populations are no longer as technologically challenging or resource-intensive as they once were. Significant progress has also been made in epigenomics, transcriptomics, proteomics, metabolomics, and phenomics, offering new opportunities in plant genomics research. Although generating genome sequencing data is no longer a primary limitation, vast amounts of genomic data are now deposited in public databases. The new challenge in the genomic era lies in navigating this vast sea of data to extract meaningful insights. Each plant genome consists of hundreds of millions to trillions of bases, containing tens of thousands of genes and numerous non-coding elements. To date, only a small fraction of plant genomes, even in model species like /Arabidopsis/, has been fully characterized. In this Special Issue, we invite dedicated scientists to submit their recent research and review articles on plant genomics and genetics, supported by functional analyses, in order to promote further exploration and conversation regarding these subjects.

Prof. Dr. Hon-Ming Lam
Dr. Sachiko Isobe
Dr. Man-Wah Li
Guest Editors

Manuscript Submission Information

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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

  • genome sequencing
  • optical mapping
  • genome editing
  • population genomics
  • genome-wide
  • association mapping
  • functional genomics
  • epigenomics
  • genetic interaction
  • chromatin
  • biodiversity

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Published Papers (2 papers)

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16 pages, 3418 KiB  
Article
Identification of Long-Distance Mobile mRNAs Responding to Drought Stress in Heterografted Tomato Plants
by Kanghua Du, Da Zhang, Zhong Dan, Lingfeng Bao, Wanfu Mu and Jie Zhang
Int. J. Mol. Sci. 2025, 26(7), 3168; https://doi.org/10.3390/ijms26073168 - 29 Mar 2025
Viewed by 238
Abstract
Grafting is widely used as an effective strategy to enhance tolerance to biotic and abiotic stresses and improve fruit quality in horticultural crops. However, the molecular mechanisms of transcription and the regulatory functions in response to drought stress of mobile mRNAs remain poorly [...] Read more.
Grafting is widely used as an effective strategy to enhance tolerance to biotic and abiotic stresses and improve fruit quality in horticultural crops. However, the molecular mechanisms of transcription and the regulatory functions in response to drought stress of mobile mRNAs remain poorly understood. In this study, we developed a grafting system based on the “one grafted plant—three samples” approach using the cultivated tomato/Solanum pennellii (Heinz 1706/LA 0716) heterografting system. A bioinformatics pipeline was developed based on RNA-seq to identify mobile mRNAs in the heterografting systems. A total of 61 upwardly and 990 downwardly mobile mRNAs were identified. Furthermore, we found that the mobility of mRNAs was not correlated with their abundance. The functional annotation and enrichment analysis indicated that mobile mRNAs were mainly involved in RNA binding, photosynthesis, photosystem, response to heat, and translation processes, and ultimately increased the drought tolerance of grafted plants. In addition, we also analyzed the RNA-binding proteins (RBPs) of downwardly mobile mRNAs and found that RBPs were conserved among species. Further, mobile mRNAs may be degraded during transportation. This study provides a pipeline for detecting mobile mRNAs in plant heterografting systems and offers new insights into future studies on long-distance mRNAs transport and regulatory mechanisms involved in drought stress responses. Full article
(This article belongs to the Special Issue Power Up Plant Genetic Research with Genomic Data: 3rd Edition)
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23 pages, 7701 KiB  
Article
Comparative Analysis of Complete Chloroplast Genomes and Phylogenetic Relationships in Medicinally Important Pantropical Genus Bauhinia s.s. (Leguminosae) from Southern Africa and Eastern Asia
by Yanxiang Lin, Yuan Chen, Yanlin Zhao, Wei Wu, Chengzi Yang, Yanfang Zheng and Mingqing Huang
Int. J. Mol. Sci. 2025, 26(1), 397; https://doi.org/10.3390/ijms26010397 - 5 Jan 2025
Viewed by 1051
Abstract
Bauhinia s.s. belongs to the Cercidoideae subfamily, located at the base of the Leguminosae family. It displays a variety of growth habits and morphologies, and is widely utilized as both ornamental and medicinal plants globally. The objective of this research is to uncover [...] Read more.
Bauhinia s.s. belongs to the Cercidoideae subfamily, located at the base of the Leguminosae family. It displays a variety of growth habits and morphologies, and is widely utilized as both ornamental and medicinal plants globally. The objective of this research is to uncover chloroplast genomes of species from Eastern Asia and Southern Africa, thereby advancing our understanding of the diversity within this genus. This study sequenced Bauhinia purpurea, Bauhinia brachycarpa var. microphylla, Bauhinia variegata var. candida, Bauhinia galpinii, and Bauhinia monandra using the Illumina platform and conducted the construction of phylogenetic trees as well as the estimation of divergence times. Compared to Asian species, the IR regions of African species underwent a contraction of approximately 100–400 bp. The phylogenetic analysis indicated that Asian and African species clustered into two distinct clades, with high support. The divergence of Bauhinia s.s. species occurred in the late Paleocene, and the rps18 and cemA genes were under positive selection. Six hypervariable regions were screened for evolutionary studies and the super-barcode data were used for species delimitation. The results revealed certain differences between African and Asian species in their chloroplast genomes of Bauhinia species. Full article
(This article belongs to the Special Issue Power Up Plant Genetic Research with Genomic Data: 3rd Edition)
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