Mutations are raw materials for evolution. Detecting mutations precisely and comprehensively is a challenge due to the repeat nature of plant genomes. Haplotype-resolved T2T assembly is the perfect foundation for variant calling. I am working on variant calling with population-scale assemblies by pangenome graphs. Adaptive complex genome rearrangements cannot simply represent by pairwise comparisons within two individuals. How to accurately represent the multi-allele and complex nature of these variants remain an open problem. The consequence of complex rearrangements brings the birth and death of coding gene. Annotating gene with high accuracy and then combining it into the pangenome graph is the new challenge in the pangenome era.