Harnessing super pan-genomics for accelerated crop improvement

While a pan-genome that reflects the genetic diversity within a species is fundamental to crop improvement, a super pan-genome adds a dimension by capturing the genetic diversity of a crop species together with its wild relatives, thereby providing a solid foundation for genetic improvement. In this review, we introduce the concepts of the pan-genome and super pan-genome and compare three commonly used construction strategies: de novo assembly, iterative assembly, and the variation graph approach. We also summarize currently available major data analysis and visualization tools and compare gene-based and sequence-based pan-genomes and super pan-genomes. Finally, we discuss the applications of super pan-genomes in crop breeding and propose future research directions.