National Key Laboratory for Germplasm Innovation Utilization of Horticultural Crops, The College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan 430070, China.
Florida Museum of Natural History, University of Florida, Gainesville, FL 32611.
Proc Natl Acad Sci U S A. 2024 Jun 11;121(24):e2319679121. doi: 10.1073/pnas.2319679121. Epub 2024 Jun 3.
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, × (London planetree; Platanaceae) is a widely used street tree. Given the pivotal phylogenetic position of and its 2-y flowering transition, understanding its flowering-time regulatory mechanism has significant evolutionary implications; however, the impact of genome evolution on flowering-time genes remains unknown. Here, we assembled a high-quality, chromosome-level reference genome for × using a phylogeny-based subgenome phasing method. Comparative genomic analyses revealed that . × (2 = 42) is an ancient hexaploid with three subgenomes resulting from two sequential WGD events; does not seem to share any WGD with other Proteales or with core eudicots. Each . × subgenome is highly similar in structure and content to the reconstructed pre-WGD ancestral eudicot genome without chromosomal rearrangements. The . × genome exhibits karyotypic stasis and gene sub-/neo-functionalization and lacks subgenome dominance. The copy number of flowering-time genes in 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 . The . × reference genome will greatly expand understanding of the evolution of genome organization, genetic diversity, and flowering-time regulation in angiosperms.
全基因组复制（WGD；即多倍体）和染色体重排（即基因组改组）显著影响基因组结构和组织。许多多倍体与它们的 WGD 祖先相比表现出广泛的基因组改组。目前还没有 Platanaceae（悬铃木目）的参考基因组，Platanaceae 是核心真双子叶植物的姐妹群之一。此外，Platanus occidentalis （伦敦悬铃木；悬铃木科）是一种广泛使用的行道树。鉴于 和其 2 年开花的过渡在系统发育上的关键位置，了解其开花时间调控机制具有重要的进化意义；然而， 基因组进化对开花时间基因的影响尚不清楚。在这里，我们使用基于系统发育的亚基因组分相方法为 × 组装了一个高质量的染色体水平参考基因组。比较基因组分析表明， × （2n = 42）是一个古老的六倍体，有三个亚基因组是由两次连续的 WGD 事件产生的； 似乎与其他悬铃木目或核心真双子叶植物没有共享任何 WGD。每个 × 亚基因组在结构和内容上与重建的 pre-WGD 祖先真双子叶植物基因组高度相似，没有染色体重排。 × 基因组表现出核型静止和基因亚/新功能化，并且缺乏亚基因组优势。与其他非核心真双子叶植物相比，开花时间基因的拷贝数在 中发生了扩张，主要是通过 WGD 事件。重复基因的亚/新功能化提供了独特的开花时间调控的遗传基础。 × 参考基因组将极大地扩展人们对被子植物基因组组织、遗传多样性和开花时间调控进化的理解。
