With the rapid advancement of forest tree genomics, particularly in pan-genome and multi-omics technologies, research on plant gene families is entering a new era. Pan-genomics breaks the limitations of a single reference genome, revealing richer genetic diversity within and between species. The integration of multi-omics provides unprecedented multidimensional perspectives for systematically deciphering gene function, regulatory networks, and evolutionary mechanisms. In this context, trees, as perennial organisms with complex morphology and significant ecological and economic value, warrant in-depth exploration of the evolution and function of their gene families. However, compared to annual model plants or crops, there remains much unknown regarding the evolutionary adaptation, regulatory complexity, and functional diversity of tree gene families. This is especially true for biological processes unique to woody plants (e.g., wood formation, longevity, stress memory), where the expansion, contraction, functional innovation, and regulatory mechanisms of gene families await systematic elucidation.

Topics of interest include, but are not limited to:

This special issue, organized by Forestry Research Advances (FRA), aims to advance tree gene family research across multiple dimensions: pan-genomics, comparative genomics, multi-omics integration, spatio-temporal dynamics, epigenetic regulation, and synthetic biology. We warmly invite original research, reviews, methods, and perspectives on:

1. Gene family analysis from the perspective of pan-genomics and evolutionary adaptation. Analyze gene family expansion/contraction, positive selection, and neofunctionalization using pan/super-pan-genomes. Link family variations to adaptive traits (e.g., NLR disease resistance genes, stress response) for breeding targets.

2. Comparative genomics of gene families in trees and annual plants. Investigate gene family evolution in divergence of woody/herbaceous growth patterns through comparative genomics of closely related species.

3. Gene family analysis from a multi-omics and systems biology perspective. Systematically dissect functional differentiation, regulatory networks, and evolution of gene families by integrating genomics, transcriptomics, proteomics, metabolomics, and epigenomics.

4. Evolution and functional innovation of non-coding RNA gene families.  Study ncRNA family expansion, sequence evolution, and regulatory innovation in development, stress response, and species-specific adaptation. Explore co-evolution with protein-coding gene families.

5. Gene family analysis with spatiotemporal dynamics and single-cell resolution. Decipher dynamic expression patterns of gene families across cell types, tissue development, and environmental responses using single-cell/spatial transcriptomics. Map expression at single-cell resolution to identify key cell-type-specific members.

6. Gene family analysis from the perspective of 3D genomics and epigenetic regulation. Analyze coordinated regulation, chromatin openness evolution, and contributions to neofunctionalization from chromatin architecture, histone modifications, and DNA methylation.

7. Synthetic biology and gene family engineering.  Employ artificial intelligence (AI) and machine learning (ML)-driven protein engineering to design artificial genetic pathways. Rationally engineer gene family members to optimize metabolic pathways (e.g., secondary metabolite synthesis).

8. New algorithms and platforms for gene family analysis.  Develop efficient algorithms (especially AI-based) for gene family identification, functional annotation, synteny analysis, and positive selection detection. Build automated pipelines and integrated platforms for the entire workflow from identification to functional prediction.

Submissions beyond these themes but aligned with the special issue’s focus are welcome. We encourage leveraging emerging omics technologies, computational tools, and experimental approaches to uncover gene family roles in tree evolution, development, adaptation, and functional regulation.

This issue aims to foster academic exchange and collaboration in tree gene family research, providing theoretical and methodological foundations for forestry science and molecular design breeding.

Guest Editors: 

Prof. Dr. Shihui Niu, College of Biological Sciences and Technology, Beijing Forestry University, China

Prof. Dr. Liuyin Ma, Haixia Institute of Science and Technology, Fujian Agriculture and Forestry, China

Deadline

The deadline for manuscript submissions is 31 December 2026, but we can accommodate extensions on a case-by-case basis. All papers will be published as open access articles upon acceptance.

Submission Instructions

Please submit the full manuscript to Forestry Research Advances via our Online Submission System. All manuscripts are thoroughly refereed through a single-anonymized peer-review process. A guide for authors for submission of manuscripts is available on the For Authors page.

Additionally, please choose the topic of this Special Issue when submitting and specify it in your cover letter. For further inquiries, please contact Guest Editors:

Shihui Niu (arrennew@bjfu.edu.cn)

Liuyin Ma (lma223@fafu.edu.cn)