Haplotype-Resolved Assembly in Polyploid Plants: Methods, Challenges, and Implications for Evolutionary and Breeding Research.

Polyploidization has been one of the key drivers of plant evolution, profoundly influencing plant adaptation in nature and crop traits in agriculture. Deciphering polyploid genomes is a crucial step for understanding evolutionary history and advancing agricultural applications. However, the inherent complexity of polyploid genomes has long hindered accurate assembly and annotation. Recent advances in sequencing technologies and improved assembly algorithms have significantly enhanced the resolution of complex polyploid genomes. These innovations have led to the successful assembly and public release of an increasing number of high-quality polyploid plant genomes. This review summarizes the mechanisms of polyploid formation and their evolutionary relevance, with a focus on recent technological progress in sequencing and genome assembly. On this basis, we further discuss the current key challenges of polyploid genome assembly and the ways to address them.