Song Baoxing's research group has published a review article entitled "New whole-genome alignment tools are needed for tapping into plant diversity" in Trends in Plant Science. The article systematically summarized the algorithms of genome comparison software developed over decades; for the first time based on the characteristics of plant genomes, it introduced the concept of whole-genome duplication-aware alignment methods; elucidated the universality and importance of multiple alleles; and looked forward to the technical challenges and development directions faced in the era of novel genome assembly at plant population scale, conducting in-species and inter-species genome comparisons along with quantitative and population genetics analysis.