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

• 成果类型: Article
• 署名作者: Yan, Xu; Shi, Gehui; Sun, Miao; Shan, Shengchen; Chen, Runzhou; Li, Runhui; Wu, Songlin; Zhou, Zheng; Li, Yuhan; Liu, Zhenhua; Hu, Yonghong; Liu, Zhongjian; Soltis, Pamela S.; Zhang, Jiaqi; Soltis, Douglas E.; Ning, Guogui; Bao, Manzhu
• 署名单位: Huazhong Agricultural University; State University System of Florida; University of Florida; Chinese Academy of Sciences; Fujian Agriculture & Forestry University; State University System of Florida; University of Florida; State University System of Florida; University of Florida; State University System of Florida; University of Florida
• 刊物名称: PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
• ISSN/ISSBN: 0027-12590
• DOI: 10.1073/pnas.2319679121
• 发表日期: 2024-06-11
• 关键词: expression pattern; plant; gene; database; alignment; tool; identification; fractionation; duplication; divergence

摘要

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 r eference genome is currently available for Platanaceae (Proteales), one of the sister groups to the core eudicots. Moreover, Platanus x 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. x acerifolia using a phylogeny - based subgenome phasing method. Comparative genomic analyses revealed that P . x 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 . x acerifolia subgenome is highly similar in structure and content to the reconstructed pre - WGD ancestral eudicot genome without chromosomal rearrangements. The P . x acerifolia genome exhibits karyotypic stasis and gene sub - /neo - functionalization and lacks subgenome dominance. The copy number of flowering - time genes in P. x acerifolia has undergone an expansion compared to other noncore eudicots, mainly via the WGD events. Sub - /neo - functionalization of duplicated genes provided the genetic basis underlying the unique flowering - time regulation in P. x acerifolia . The P . x acerifolia reference genome will greatly expand understanding of the evolution of genome organization, genetic diversity, and flowering - time regulation in angiosperms.