Plant Pan-Genomics: Opportunities, Advances, and Challenges

The pan-genome concept encompasses all individual genome sequences within a species, comprising both core and variable genes. In recent years, it has emerged as a promising avenue for advancing plant genetic evolution and cultivating desirable traits. This review provides a comprehensive overview of pan-genome representation, detailing both linear pan-genome and graph-based pan-genome. It further presents a thorough analysis of the assembly methods for these pan-genomic structures and discusses the widely used software tools and processes for their construction, including VG, Minigraph, and PGGB. The paper concurrently delineates the fundamental factors that influence pan-genome quality, which include genome assembly quality, accurate annotation, identification of homologous genes, and strategic sample selection. Furthermore, we investigate the pan-genome's applications in plant genomics and provide a summary of recent research findings related to the plant pan-genomes, particularly in elucidating genetic transformations during domestication, uncovering genetic variations linked to agronomic traits, and offering insights to guide breeding endeavors.   Received: 14 April 2024 | Revised: 13 May 2024| Accepted: 4 June 2024   Conflicts of Interest The authors declare that they have no conflicts of interest to this work.   Data Availability Statement Data sharing is not applicable to this article as no new data were created or analyzed in this study.   Author Contribution Statement Mingjun Hou: Conceptualization, Methodology, Software, Validation, Formal analysis, Investigation, Resources, Data curation, Writing - original draft, Writing - review & editing, Visualization, Supervision, Project administration. Shaozi Pang: Writing - review & editing, Visualization, Supervision.