The Developments and Prospects of Plant Super Pangenomes: Demands, Approaches and Applications

By integrating genomes of different accessions, the pangenome can offer more comprehensive and reference-bias-free population genetic information in a species than a single reference genome. With the rapid accumulation of genomic sequencing data and the expanding scope of plant research, the focus of plant pangenomics research has gradually evolved from a single species to multiple species in recent years, giving rise to the concept of super pangenome that cover all genomic sequences of a genus-level taxonomic groups. By integrating more cultivated and wild species, the super pangenome has made significant contributions to the resolution of multiple research areas such as plant genetic diversity, evolution, domestication, and molecular breeding. Here, we provide a comprehensive overview of the plant super pangenomes, focusing on its unique value and development demands, construction approaches, potential applications and achievements. We highlight the distinctive advantages and promising prospects of super pangenomes and discuss the current challenges and future directions. Short Summary: By incorporating a broader range of cultivated and wild species, the plant super pangenome has significantly advanced multiple research areas. Here, we systematically summarize the developments and prospects of the plant super pangenomes, emphasizing their unique value, developmental demands, construction approaches, potential applications and notable achievements. We highlight the distinctive advantages, promising outlook and future directions of this emerging field.