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Advancements and Trends in Plant Genomics
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Advancements and Trends in Plant Genomics

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: 20 September 2026 | Viewed by 3738

Special Issue Editor

Dr. Rongbin Hu

E-Mail Website
Guest Editor
Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
Interests: plant genomics

Special Issue Information

Dear Colleagues,

Recent advancements in plant genomics have revolutionized our understanding of plant biology, adaptation, and crop improvement. Next-generation sequencing (NGS) and third-generation sequencing (TGS) technologies have enabled high-resolution genome assembly, uncovering novel genes and regulatory elements. Pangenomics and comparative genomics have deepened our insights into genetic diversity, identifying traits linked to stress tolerance, yield enhancement, and disease resistance. CRISPR-Cas genome editing has revolutionized functional genomics, enabling precise gene modifications to accelerate breeding and develop climate-resilient crops. Meanwhile, single-cell and spatial transcriptomics are revealing cell-type-specific gene expression patterns, shedding light on development and plant–environment interactions. The integration of multi-omics approaches—genomics, transcriptomics, epigenomics, proteomics, and metabolomics—has unraveled complex regulatory networks controlling plant growth and metabolism. Machine learning and artificial intelligence are also enhancing the analysis of genomic datasets, improving gene function prediction and trait selection. Emerging trends include synthetic biology for designing novel traits, digital genomics for precision agriculture, and leveraging genomic data for sustainable crop production, addressing global food security and environmental challenges. We invite researchers to contribute to our Special Issue, “Advancements and Trends in Plant Genomics”.

We welcome original research articles and reviews on genomic discoveries, methodological innovations, and functional insights, particularly studies integrating multi-omics, genome editing, computational genomics, and crop improvement applications. We invite you to share your findings and participate in advancing plant science, fostering collaboration, and driving innovation in sustainable agriculture and biodiversity conservation. Please consider submitting your manuscript to our Special Issue.

Dr. Rongbin Hu
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
  • genomics
  • next-generation sequencing
  • third-generation sequencing
  • CRISPR-Cas

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Published Papers (4 papers)

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Research

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20 pages, 3086 KB  
Article
Rhythmic Mechanisms Governing CAM Photosynthesis in Kalanchoe fedtschenkoi: High-Resolution Temporal Transcriptomics
by Rongbin Hu, Sara Jawdy, Avinash Sreedasyam, Anna Lipzen, Mei Wang, Vivian Ng, Christopher Daum, Keykhosrow Keymanesh, Degao Liu, Alex Hu, Asher Pasha, Nicholas J. Provart, Anne M. Borland, Timothy J. Tschaplinski, Gerald A. Tuskan, Jeremy Schmutz and Xiaohan Yang
Int. J. Mol. Sci. 2026, 27(3), 1342; https://doi.org/10.3390/ijms27031342 - 29 Jan 2026
Viewed by 641
Abstract
Crassulacean acid metabolism (CAM) is a specialized photosynthetic pathway that enhances water-use efficiency by temporally separating nocturnal CO2 uptake from daytime decarboxylation and carbon fixation. To uncover the regulatory mechanisms coordinating these temporal dynamics, we generated high-resolution, 48 h time-course transcriptomes for [...] Read more.
Crassulacean acid metabolism (CAM) is a specialized photosynthetic pathway that enhances water-use efficiency by temporally separating nocturnal CO2 uptake from daytime decarboxylation and carbon fixation. To uncover the regulatory mechanisms coordinating these temporal dynamics, we generated high-resolution, 48 h time-course transcriptomes for the CAM model Kalanchoe fedtschenkoi under both 12 h/12 h light/dark (LD) cycles and continuous light (LL). A rhythmicity analysis revealed that diel light cues are the dominant driver of transcript oscillations: 16,810 genes (54.3% of annotated genes) exhibited rhythmic expression only under LD, whereas just 399 genes (1.3%) remained rhythmic under LL. A smaller set of 3009 genes (9.7%) oscillated in both conditions, indicating that the intrinsic circadian clock sustains rhythmicity for a limited subset of the transcriptome. A gene co-expression network analysis revealed extensive integration between circadian clock components, core CAM pathway enzymes, and stomatal regulators, defining regulatory modules that coordinate metabolic and physiological timing. Notably, key hub genes associated with post-translational and post-transcriptional regulation, including the E3 ubiquitin ligase HUB2 and several pentatricopeptide repeat (PPR) proteins, act as central nodes in CAM-associated networks. This discovery implicates epigenetic and organellar regulation as previously unrecognized critical tiers of control in CAM. Together, our results support a regulatory model in which CAM rhythmicity is governed by both external light/dark cues and the endogenous circadian clock through multi-level control spanning transcriptional and protein-level regulation. To support community exploration, we also provide an interactive eFP (electronic Fluorescent Pictograph) browser for visualizing time-resolved gene expression profiles. Full article
(This article belongs to the Special Issue Advancements and Trends in Plant Genomics)
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15 pages, 1809 KB  
Article
Comparison of Genomes of Species from Polemonium caeruleum Complex and Polemonium pulcherrimum Complex Based on Repeatome and Chromosome Analysis
by Olga V. Muravenko, Alexandra V. Amosova, Alexey R. Semenov, Ekaterina D. Badaeva, Julia V. Kalnyuk, Svyatoslav A. Zoshchuk and Olga Yu. Yurkevich
Int. J. Mol. Sci. 2026, 27(1), 229; https://doi.org/10.3390/ijms27010229 - 25 Dec 2025
Viewed by 639
Abstract
Polemonium L. (Polemoniaceae) is a widespread genus native to subarctic and arctic regions of the Northern Hemisphere. The taxonomy and genome relationships within Polemonium are still unclear. We analyzed genomes of three species from each Polemonium caeruleum and Polemonium pulcherrimum complex using bioinformatic [...] Read more.
Polemonium L. (Polemoniaceae) is a widespread genus native to subarctic and arctic regions of the Northern Hemisphere. The taxonomy and genome relationships within Polemonium are still unclear. We analyzed genomes of three species from each Polemonium caeruleum and Polemonium pulcherrimum complex using bioinformatic analysis by RepeatExplorer2/TAREAN pipelines of next-generation sequencing data. The repeatomes of all studied species were similar in type and number of repeats. Satellite DNAs (satDNAs) demonstrated high sequence identity within the studied species. FISH chromosome mapping of 45S rDNA, 5S rDNA, and two satDNAs Pol_C 33 and Pol_C 46 allowed us to construct the species karyograms and assess the genome diversity within the P. caeruleum complex and P. pulcherrimum complex, and also confirm the taxonomic status of P. kiushianum as an independent species. Our findings demonstrate a close genomic relationship among the species from P. caeruleum and P. pulcherrimum complexes, indicating the presence of a common ancestral genome; additionally, our results provide cytogenetic evidence for the monophyletic origin of these sections and also complex evolutionary history of the genus Polemonium. The developed approach may be a valuable framework for further investigation of the chromosomal organization of karyotypes in other species of the genus Polemonium. Full article
(This article belongs to the Special Issue Advancements and Trends in Plant Genomics)
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Review

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29 pages, 2995 KB  
Review
Molecular Regulators of In Vitro Regeneration in Wheat: Roles of Morphogenic Factors in Transformation, Genome Editing, and Breeding
by Sylwia Kowalik, Monika Samoń and Mateusz Przyborowski
Int. J. Mol. Sci. 2026, 27(3), 1271; https://doi.org/10.3390/ijms27031271 - 27 Jan 2026
Cited by 1 | Viewed by 926
Abstract
Efficient in vitro regeneration remains a major constraint in the genetic transformation, genome editing, and molecular breeding of wheat (Triticum aestivum L.), largely due to strong genotype-dependent recalcitrance and limited activation of developmental programs required for somatic embryogenesis. Plant regeneration relies on [...] Read more.
Efficient in vitro regeneration remains a major constraint in the genetic transformation, genome editing, and molecular breeding of wheat (Triticum aestivum L.), largely due to strong genotype-dependent recalcitrance and limited activation of developmental programs required for somatic embryogenesis. Plant regeneration relies on extensive transcriptional reprogramming and epigenetic remodeling orchestrated by morphogenic regulators that modulate meristem identity, as well as cellular pluri- and totipotency. In this review, we synthesize current molecular knowledge on key transcription factors (BBM, WUS/WUS2, GRF-GIF, WOX, LAX1, SERK, WIND1/ERF115) and signaling peptides (CLE/CLV-WUS module, phytosulfokine/PSK) that regulate embryogenic competence in monocot cereals, with emphasis on their orthologs and functional relevance in wheat. We highlight how controlled expression of these morphogenic genes, promoter engineering, and transient or excisable induction systems can significantly enhance regeneration capacity, reduce chimerism in CRISPR-Cas-edited plants, and facilitate genotype-independent transformation. We also discuss epigenetic and metabolic constraints underlying wheat recalcitrance and their potential modulation to improve culture responsiveness. By integrating evidence from wheat, rice, maize, and barley, we outline conserved gene-regulatory networks that reinitiate totipotency and propose strategies to accelerate doubled haploid production and speed-breeding pipelines. Collectively, morphogenic factors emerge as central molecular tools for overcoming regeneration bottlenecks and enabling next-generation wheat improvement. The objective of this review is to synthesize and critically evaluate current molecular knowledge on morphogenic regulators controlling in vitro regeneration in wheat (Triticum aestivum L.), with particular emphasis on their roles in genetic transformation and genome editing. Full article
(This article belongs to the Special Issue Advancements and Trends in Plant Genomics)
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21 pages, 1955 KB  
Review
Host Factors Promoting the LTR Retrotransposon Life Cycle in Plant Cells: Current Knowledge and Future Directions
by Pavel Merkulov, Alexander Polkhovskiy, Elizaveta Kamarauli, Kirill Tiurin, Alexander Soloviev and Ilya Kirov
Int. J. Mol. Sci. 2026, 27(1), 374; https://doi.org/10.3390/ijms27010374 - 29 Dec 2025
Viewed by 960
Abstract
Long Terminal Repeat (LTR) retrotransposons (LTR-RTEs) comprise up to 90% of some plant genomes and drive genome diversification through their amplification. Novel insertions arise during the final stages of the LTR-RTE life cycle, which depends on both LTR-RTE-encoded proteins and host cellular factors. [...] Read more.
Long Terminal Repeat (LTR) retrotransposons (LTR-RTEs) comprise up to 90% of some plant genomes and drive genome diversification through their amplification. Novel insertions arise during the final stages of the LTR-RTE life cycle, which depends on both LTR-RTE-encoded proteins and host cellular factors. The LTR-RTE elements require host transcriptional machinery for RNA production, followed by nuclear processing/export, translation, virus-like particle assembly, reverse transcription, and genomic integration. This review addresses the following question: What host proteins promote LTR-RTE transposition in plants? Our analysis of recent literature on host factors and cellular compartments implicated in the retrotransposition cycle reveals the extensive integration of LTR-RTEs into host processes. Nonetheless, the precise mechanisms remain poorly resolved, especially in plants with their rich repertoire of LTR-RTEs. We propose integrating plant mobilomics with transposition reporters, genome editing, synthetic biology, and interactomics to elucidate plant-specific mechanisms. Full article
(This article belongs to the Special Issue Advancements and Trends in Plant Genomics)
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