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Biology
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Advances in Plant Multi-Omics
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Advances in Plant Multi-Omics

A special issue of Biology (ISSN 2079-7737). This special issue belongs to the section "Plant Science".

Deadline for manuscript submissions: 31 October 2026 | Viewed by 4415

Special Issue Editors

Dr. Xiuzhang Li

E-Mail Website
Guest Editor
State Key Laboratory of Plateau Ecology and Agriculture, Qinghai Academy of Animal and Veterinary Science, Qinghai University, Xining 810016, China
Interests: plant stress biology; edible and medicinal fungi; grass endophyte; multi-omics
Special Issues, Collections and Topics in MDPI journals
Dr. Zhonglong Guo

E-Mail Website
Guest Editor
State Key Laboratory of Plant Diversity and Specialty Crops, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
Interests: bioinformatics; multi-omics; microRNA
Dr. Xuekai Wei

E-Mail Website
Guest Editor
College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou 730020, China
Interests: poisonous grass; poisonous grass prevention and control; grass endophyte

Special Issue Information

Dear Colleagues,

With the rapid development of high-throughput sequencing, mass spectrometry, and bioinformatics technologies, plant research has advanced from single "omics" to the era of multi-omics integration. By comprehensively analyzing multi-dimensional data including genomics, transcriptomics, proteomics, metabolomics, epigenomics, and microbiomics, plant multi-omics provides a novel perspective for deciphering the regulatory mechanisms of plant growth and development, stress response pathways, quality formation patterns, and evolutionary adaptation strategies.

However, current plant multi-omics research still faces critical challenges such as a low efficiency of data integration, insufficient cross-scale mechanism interpretation, and a delayed translation of theoretical achievements into practical applications. To address these gaps, the journal Biology (Impact Factor: 3.5, JCR Q1) plans to launch a Special Issue entitled "Advances in Plant Multi-Omics". This Special Issue emphasizes full-chain innovation in plant multi-omics research, covering "technological method breakthroughs, in-depth mechanism interpretation, and industrial application translation". Special attention is paid to the practical value of multi-omics technologies in addressing key issues in agricultural production (e.g., stress-resistant breeding, quality improvement) and ecological conservation (e.g., species adaptability, community interaction). We hereby sincerely invite scholars worldwide in related fields to submit manuscripts, jointly building a systematic academic platform for plant multi-omics research.​

This Special Issue accepts various types of research, including but not limited to the following directions, covering both basic and applied research:​

  1. Innovation in multi-omics technologies and methods;
  2. Multi-omics interpretation of key biological issues;
  3. Translational research of multi-omics applications.

Dr. Xiuzhang Li
Dr. Zhonglong Guo
Dr. Xuekai Wei
Guest Editors

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. Biology is an international peer-reviewed open access semimonthly 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 2700 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

  • multi-omics integration
  • plant systems biology
  • high-throughput sequencing
  • bioinformatics integration
  • stress response

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Published Papers (6 papers)

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16 pages, 3517 KB  
Article
Transcriptome Analysis Revealed Potential Regulatory Networks Underlying Corolla Movement in Mirabilis jalapa (Nyctaginaceae)
by Dingkun Liu, Huiqi Yan, Xuan Wang, Xiaohong Yan and Bing Zhou
Biology 2026, 15(7), 585; https://doi.org/10.3390/biology15070585 - 6 Apr 2026
Viewed by 488
Abstract
Corolla movement is a typical plant movement behavior that enables plants to optimize pollination and adapt to environmental changes. Nevertheless, its molecular mechanism remains poorly understood. In the present study, we conduct a comprehensive transcriptome analysis of Mirabilis jalapa (Nyctaginaceae) corolla at five [...] Read more.
Corolla movement is a typical plant movement behavior that enables plants to optimize pollination and adapt to environmental changes. Nevertheless, its molecular mechanism remains poorly understood. In the present study, we conduct a comprehensive transcriptome analysis of Mirabilis jalapa (Nyctaginaceae) corolla at five stages (AG-EG) to elucidate the regulatory networks underlying movement. The results showed that the differentially expressed genes (DEGs) were mainly associated with cellular processes, catalytic activity, MAPK signaling, plant hormone signal transduction, and photosynthesis-related pathways, highlighting their involvement in corolla dynamics. Transcriptome profiling further demonstrated that auxin, ethylene, and abscisic acid signaling pathways were key hormonal regulators of corolla movement. Moreover, Ca2+ transport genes (CNGCs and CMLs) and respiratory burst oxidase homologs (RBOHs) were significantly enriched, indicating that Ca2+–ROS signaling oscillations also play an important role in driving differential cell expansion and turgor changes. Transcription factor analysis also revealed the upregulation of WRKY2, WRKY22, and WRKY33, suggesting that WRKYs act as the critical transcriptional regulators linking ROS–Ca2+ signals with downstream gene expression. The reliability of RNA-Seq data was confirmed by RT-qPCR, which showed high consistency with transcriptome profiles. These findings suggested that corolla movement in M. jalapa is carried through the integration of hormonal pathways, Ca2+–ROS signaling, and WRKY-mediated transcriptional regulation. This research provided novel insights into the molecular basis of plant movement and established a foundation for further study on floral dynamics and adaptive strategies in angiosperms. Full article
(This article belongs to the Special Issue Advances in Plant Multi-Omics)
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22 pages, 30473 KB  
Article
Physiological, Transcriptomic, and Metabolomic Responses of Brachiaria decumbens Roots During Symbiosis Establishment with Piriformospora indica
by Man Liu, Xinyong Li, Wenke Zhang, Xinghua Zhao, Yuehua Sun, An Hu, Rui Zhang and Kai Luo
Biology 2026, 15(3), 215; https://doi.org/10.3390/biology15030215 - 23 Jan 2026
Viewed by 639
Abstract
Brachiaria decumbens is a high-yielding forage grass of major economic value in tropical regions. The root endophytic fungus Piriformospora indica is widely recognized for promoting plant growth and stress tolerance, yet its effects on B. decumbens remain poorly characterized. Here, we profiled root [...] Read more.
Brachiaria decumbens is a high-yielding forage grass of major economic value in tropical regions. The root endophytic fungus Piriformospora indica is widely recognized for promoting plant growth and stress tolerance, yet its effects on B. decumbens remain poorly characterized. Here, we profiled root responses to P. indica colonization at 10 days after inoculation (dais; early stage) and 20 dais (late stage) during symbiosis establishment. Colonization was confirmed by phenotypic and physiological assessments, with inoculated plants showing enhanced root growth; colonized roots exhibited higher activities of catalase (CAT), superoxide dismutase (SOD), and peroxidase (POD), along with increased indole-3-acetic acid (IAA) levels, whereas malondialdehyde (MDA), jasmonic acid (JA), and the ethylene precursor 1-aminocyclopropane-1-carboxylic acid (ACC) were reduced. Transcriptome and metabolomic profiling identified 1884 and 1077 differentially expressed genes (DEGs) and 2098 and 1509 differentially accumulated metabolites (DAMs) at 10 dais (Pi10d vs. CK10d) and 20 dais (Pi20d vs. CK20d), respectively, and 3355 DEGs and 2314 DAMs between stages (Pi20d vs. Pi10d). Functional enrichment highlighted key pathways related to secondary metabolism, carbohydrate metabolism, and lipid biosynthesis. Differentially expressed transcription factors spanned multiple families, including MYB, AP2/ERF, MADS-box, and bZIP, consistent with broad transcriptional reprogramming during symbiosis establishment. Integrative multi-omics analysis further highlighted phenylpropanoid biosynthesis and α-linolenic acid metabolism as consistently co-enriched pathways, suggesting coordinated shifts in gene expression and metabolite accumulation across colonization stages. Collectively, these results provide a multi-layered resource and a framework for mechanistic dissection of the P. indica–B. decumbens interaction. Full article
(This article belongs to the Special Issue Advances in Plant Multi-Omics)
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16 pages, 3522 KB  
Article
Multi-Omics Analysis Reveals the Adaptive Responses of Lycoris aurea to Arid Stress
by Mingxin Zhu, Zhaowentao Song, Yingzan Xie, Guanghua Liu and Youwei Zuo
Biology 2026, 15(2), 195; https://doi.org/10.3390/biology15020195 - 21 Jan 2026
Viewed by 500
Abstract
Understanding how plants respond to water limitation is increasingly important under accelerating climate change. Lycoris aurea, a widely distributed ornamental and medicinal bulbous plant, frequently inhabits environments with fluctuating soil moisture, yet its molecular drought-response mechanisms remain largely unexplored. In this study, [...] Read more.
Understanding how plants respond to water limitation is increasingly important under accelerating climate change. Lycoris aurea, a widely distributed ornamental and medicinal bulbous plant, frequently inhabits environments with fluctuating soil moisture, yet its molecular drought-response mechanisms remain largely unexplored. In this study, we investigated L. aurea growing under field-based, in situ soil moisture regimes, comparing low (~20% soil water content) and high (~40% soil water content) conditions. We combined soil property assessments with high-resolution transcriptomic and untargeted metabolomic profiling to characterize the adaptive responses of bulb tissues under contrasting soil water conditions. Although total nitrogen, phosphorus, and potassium levels were comparable across treatments, soil moisture, representing the primary contrasting field condition, and soil pH, a correlated environmental factor, were significantly associated with variation in gene expression and metabolite accumulation (p < 0.05, n = 3). Transcriptome analyses identified a total of 1034 differentially expressed genes enriched in pathways related to amino acid metabolism, cuticle formation, cell wall modification, and osmotic adjustment. Metabolomic analysis identified a total of 1867 differentially expressed metabolites belonging to carboxylic acids and prenol lipids, showing alterations involved in amino acids, lipids, phenolic acids, and alkaloids associated with osmoprotection, membrane stabilization, and structural reinforcement under low soil moisture. Pathway-based integration analysis highlighted four core pathways, including “alanine, aspartate and glutamate metabolism” (p = 0.00371) and “cutin, suberine and wax biosynthesis” (p = 0.00873), as central hubs linking transcriptional regulation with metabolic reconfiguration. Gene-metabolite-soil correlation networks further demonstrated that drought adaptation arises from tightly coordinated biochemical and structural adjustments rather than shifts in nutrient acquisition. Together, this species-specific study provides a comprehensive multi-omics framework for understanding drought tolerance in L. aurea, reveals key molecular targets associated with plant resilience, and offers potential targets and insights for the conservation of drought-resilient Lycoris cultivars. Full article
(This article belongs to the Special Issue Advances in Plant Multi-Omics)
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27 pages, 6482 KB  
Article
Synergistic Responses of Forage Pea in the Germination Stage to Saline–Alkali and Drought Stress at Phenotypic, Physiological, and Non-Targeted Metabolomic Levels
by Taoxia Liu, Xiaojian Pu, Yuanyuan Zhao, Chengti Xu and Yunjie Fu
Biology 2026, 15(2), 131; https://doi.org/10.3390/biology15020131 - 12 Jan 2026
Cited by 1 | Viewed by 608
Abstract
(1) Background: This study used Qingjian No. 1 forage pea (Pisum sativum L.) as a plant material to study its metabolic mechanisms in response to different stresses, given that saline–alkali stress and drought stress often occur simultaneously in natural environments and severely [...] Read more.
(1) Background: This study used Qingjian No. 1 forage pea (Pisum sativum L.) as a plant material to study its metabolic mechanisms in response to different stresses, given that saline–alkali stress and drought stress often occur simultaneously in natural environments and severely affect the growth and yield of forage pea, while the regulatory network underlying the adaptation of forage pea to combined stress remains poorly elucidated. (2) Methods: The metabolic mechanisms of forage pea in response to different stresses were elucidated by integrating phenotypic, physiological, and metabolomic analyses. (3) Results: The results show that compared to the control, all stress treatments significantly inhibited seed germination and seedling growth, with the combined saline–alkali and drought stress exhibiting the strongest inhibitory effect. In terms of physiological and biochemical responses, peroxidase (POD) activity increased with the complexity of the stress, with the highest POD activity observed under combined saline–alkali and drought stress, showing a 61.71% increase compared to the control (p < 0.05). Non-targeted metabolomic analysis revealed that isoflavone biosynthesis, nucleotide metabolism, and cutin–suberin–wax biosynthesis are the core responsive pathways. Correlation analysis revealed that isocorydine and phosphatidylinositol phosphate showed strong positive correlations with the vigor index, main root length, and superoxide dismutase (SOD) activity, and glycerophospholipid metabolites were positively correlated with ferric ion-reducing antioxidant capacity. (4) This study deepens understanding of the stress resistance mechanisms in forage peas and provides a theoretical basis for stress-resistant forage pea breeding. Full article
(This article belongs to the Special Issue Advances in Plant Multi-Omics)
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17 pages, 5860 KB  
Article
Transcriptomics and Metabolomics Reveal Mechanisms Underlying the Adaptation of Lamiophlomis rotata to High Altitudes
by Yunzhang Xu, Sangjie Jiancuo, Xiao Luo, Yu-E Ma, Xin Wu, Zhenzhong Wu, Hengxia Yin, Shaoshan Zhang, Wenbing Li and Huachun Sheng
Biology 2025, 14(11), 1554; https://doi.org/10.3390/biology14111554 - 5 Nov 2025
Viewed by 1028
Abstract
Lamiophlomis rotata (Benth.) Kudo is a typical alpine medicinal plant. However, the mechanism underlying its adaptation to high altitudes remains incompletely understood. In this study, we integrated transcriptome and metabolome analyses. Specifically, we used third-generation sequencing for building a reference transcriptome and second-generation [...] Read more.
Lamiophlomis rotata (Benth.) Kudo is a typical alpine medicinal plant. However, the mechanism underlying its adaptation to high altitudes remains incompletely understood. In this study, we integrated transcriptome and metabolome analyses. Specifically, we used third-generation sequencing for building a reference transcriptome and second-generation sequencing for differential gene expression analysis. Our findings revealed that the activation of the hydrogen sulfide signaling pathway and the reprogramming of amino acid metabolism are probable adaptation mechanisms. Different from previous reports, the hydrogen sulfide signaling may regulate the activity of cellulose synthase in addition to enhancement of antioxidant capacity and accumulation of osmolytes. By altering the agronomic traits of plants in a cell wall remodeling-dependent manner, it enables L. rotata to adapt to alpine stress. The accumulated amino acids not only store energy-efficient organic nitrogen as precursors for the synthesis of secondary metabolites but also act as signaling molecules to activate defense responses. Additionally, we propose a potential link between the hydrogen sulfide signaling pathway and amino acid metabolism. Overall, this study systematically explores the adaptation mechanism of L. rotata to high-altitude environments, offering a novel perspective for understanding the growth, development, stress responses, and secondary metabolic processes of alpine plants. Full article
(This article belongs to the Special Issue Advances in Plant Multi-Omics)
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17 pages, 3042 KB  
Essay
A Reference Assembly for the Legume Cover Crop Smooth Vetch Vicia villosa Roth var. glabrescens
by Zhongxu Yao, Xinru Li, Yurou Wang, Yaqi Sun, Songchong Lu, Kunlong Su, Huajie Zhang, Shaoyong Yang, Guofeng Yang and Lichao Ma
Biology 2026, 15(5), 379; https://doi.org/10.3390/biology15050379 - 26 Feb 2026
Viewed by 430
Abstract
Vicia villosa Roth var. glabrescens (smooth vetch) is an economically important legume cover crop valued for its nitrogen-fixing capacity, high biomass yield, and adaptability across diverse agroecosystems. Here, we present a chromosome-scale, high-quality genome assembly of V. villosa var. glabrescens, constructed using [...] Read more.
Vicia villosa Roth var. glabrescens (smooth vetch) is an economically important legume cover crop valued for its nitrogen-fixing capacity, high biomass yield, and adaptability across diverse agroecosystems. Here, we present a chromosome-scale, high-quality genome assembly of V. villosa var. glabrescens, constructed using PacBio HiFi sequencing combined with Hi-C scaffolding. The assembly spans 3.70 Gb with a scaffold N50 of 4.69 Mb and exhibits lower heterozygosity (0.9%) compared to V. villosa Roth (3.1%). Genome analysis revealed significant expansion of long terminal repeat retrotransposons (LTR-RTs), as well as lineage-specific proliferation of miniature inverted-repeat transposable elements (MITEs) in V. villosa var. glabrescens. Comparative genomics with V. villosa Roth highlighted gene family expansions associated with trichome development, providing insights into the genetic basis of morphological and adaptive differences within the Vicia species. This reference genome provides a foundational resource for accelerating the breeding of V. villosa varieties with enhanced agronomic traits and contributes to a broader understanding of legume genomics and plant genome evolution. Full article
(This article belongs to the Special Issue Advances in Plant Multi-Omics)
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