Plant Life: Integrating Multi-Omic Approaches from Molecules to Environment

Dear Colleagues,

Building on the success of the first edition, we can announce the second volume of this Special Issue, now expanded to be broader and more integrative in scope. This edition, titled "Plant Life: Integrating Multi-Omic Approaches from Molecules to Environment", will address the growing complexity of plant physiological research by incorporating diverse omic levels and cutting-edge technologies. We invite the submission of high-quality research articles, reviews, short communications, and reports that advance our understanding of plant physiology through multi-omic integration.

Plant physiology is governed by intricate interactions between genetic, epigenetic, and environmental factors, which collectively shape plant growth, development, and stress responses. Recent technological advancements have enabled deep exploration across multiple biological levels, from ions to ecosystems. This Special Issue will highlight studies that leverage a wide spectrum of omic approaches, including ionomics, genomics, transcriptomics, metabolomics, post-transcriptional regulation, proteomics, post-translational modifications, epigenomics, and single-cell analyses, to decipher physiological mechanisms. We encourage research that not only focuses on individual omic layers but also emphasizes their integration to provide a holistic view of plant function. Key research themes include, but are not limited to, the following:

• Ionomic Level: Studies on the role of elemental composition and ion homeostasis in plant nutrition, signaling, and adaptation to environmental stresses such as salinity, heavy metals, or nutrient deficiencies;
• Genomic Level: Research on genetic variation, genome architecture, gene families, and genome-editing applications (e.g., CRISPR/Cas9) for trait improvement or mechanistic insights into developmental processes;
• Transcriptomic Level: Investigations into gene expression dynamics, alternative splicing, non-coding RNAs, and transcriptional networks underlying plant growth, development, and responses to biotic/abiotic stresses;
• Metabolomic Level: Analyses of metabolic pathways, metabolite profiling, and flux analysis to link biochemical changes to physiological outcomes, such as in secondary metabolism or stress resilience;
• Post-Transcriptional Level: Research on RNA processing, stability, and regulation by miRNAs, siRNAs, or other factors that influence gene expression beyond transcription;
• Proteomic Level: Studies on protein expression, protein–protein interactions, and structural proteomics to elucidate functional mechanisms in signaling, metabolism, or stress adaptation;
• Post-Translational Level: Research into modifications including phosphorylation, ubiquitination, or glycosylation, as well as their roles in regulating protein activity and cellular responses;
• Epigenetic Level: Explorations of DNA methylation, histone modifications, and chromatin remodeling in gene regulation, memory responses, and transgenerational inheritance under environmental cues;
• Single-Cell Level: Applications of single-cell omics (e.g., scRNA-seq, scATAC-seq) to resolve cellular heterogeneity in tissues, organs, or during development, providing unprecedented resolution in plant physiology.

We welcome contributions that employ innovative technologies such as multi-omic integration (e.g., combining genomics with metabolomics), advanced imaging, high-throughput sequencing, and computational modeling. Studies focusing on plant–environment interactions, including responses to climate change, pathogen attacks, symbiosis, or nutrient availability, are particularly encouraged. Additionally, we request papers that address physiological mechanisms in diverse plant species, ranging from crops to model organisms, with implications for agriculture, biotechnology, and ecosystem sustainability.

This Special Issue will feature up-to-date reviews and original research that bridge omic data with physiological phenotypes, fostering a mechanistic understanding of plant life. By bringing together experts in the field, we will showcase the latest advances, challenges, and future directions in plant physiology research.

Dr. Sen Meng
Dr. Fang He
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. Life 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.

• plant physiology
• multi-omics integration
• ionomics
• genomics
• transcriptomics
• metabolomics
• proteomics
• epigenetics
• single-cell analysis
• environmental stress
• molecular mechanisms
• systems biology