Genome evolution of the ancient hexaploid Platanus × acerifolia (London planetree)

作者：Xu Yan, Gehui Shi, Miao Sun, Shengchen Shan, Runzhou Chen, Runhui Li, Songlin Wu, Zheng Zhou, Yuhan Li, Zhenhua Liu, Yonghong Hu, Zhong‐Jian Liu, Pamela S. Soltis, Jiaqi Zhang, Douglas E. Soltis, Guogui Ning, Manzhu Bao · 发表于：Proceedings of the National Academy of Sciences · 年份：2024 · DOI：10.1073/pnas.2319679121 · 被引用次数：18 · 研究领域：Chromosomal and Genetic Variations、Genomics and Phylogenetic Studies、Plant Reproductive Biology

Whole-genome duplication (WGD; i.e., polyploidy) and chromosomal rearrangement (i.e., genome shuffling) significantly influence genome structure and organization. Many polyploids show extensive genome shuffling relative to their pre-WGD ancestors. No reference genome is currently available for Platanaceae (Proteales), one of the sister groups to the core eudicots. Moreover, Platanus × acerifolia (London planetree; Platanaceae) is a widely used street tree. Given the pivotal phylogenetic position of Platanus and its 2-y flowering transition, understanding its flowering-time regulatory mechanism has significant evolutionary implications; however, the impact of Platanus genome evolution on flowering-time genes remains unknown. Here, we assembled a high-quality, chromosome-level reference genome for P. × acerifolia using a phylogeny-based subgenome phasing method. Comparative genomic analyses revealed that P . × acerifolia (2 n = 42) is an ancient hexaploid with three subgenomes resulting from two sequential WGD events; Platanus does not seem to share any WGD with other Proteales or with core eudicots. Each P . × acerifolia subgenome is highly similar in structure and content to the reconstructed pre-WGD ancestral eudicot genome without chromosomal rearrangements. The P . × acerifolia genome exhibits karyotypic stasis and gene sub-/neo-functionalization and lacks subgenome dominance. The copy number of flowering-time genes in P. × acerifolia has undergone an expansion compared to...