Understanding the underlying mechanisms and links between genome evolution and adaptive innovations stands as a key goal in evolutionary studies. Poplars, among the world’s most widely distributed and cultivated trees, exhibit extensive phenotypic diversity and environmental adaptability. In this study, we present a genus-level super-pangenome comprising 19 genomes, revealing the likely pivotal role of private genes in facilitating local environmental and climate adaptation. Through the integration of pangenomes with transcriptomes, methylomes, and chromatin accessibility mapping, we unveil that the evolutionary trajectories of pangenes and duplicated genes are closely linked to local genomic landscapes of regulatory and epigenetic architectures, notably CG methylation in gene-body regions. Further comparative genomic analyses have enabled the identification of 142 202 structural variants across species that intersect with a significant number of genes and contribute substantially to both phenotypic and adaptive divergence. We have experimentally validated a ∼180-bp presence/absence variant affecting the expression of the gene, crucial for leaf serration formation. Finally, we developed a user-friendly web-based tool encompassing the multi-omics resources associated with the super-pangenome (). Together, the present pioneering super-pangenome resource in forest trees not only aids in the advancement of breeding efforts of this globally important tree genus but also offers valuable insights into potential avenues for comprehending tree biology.

中文翻译：

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杨树的超全基因组揭示了其在广泛的森林树木中的适应和多样化的基因组方面

了解基因组进化和适应性创新之间的潜在机制和联系是进化研究的一个关键目标。杨树是世界上分布和栽培最广泛的树木之一，表现出广泛的表型多样性和环境适应性。在这项研究中，我们提出了一个包含 19 个基因组的属级超泛基因组，揭示了私有基因在促进当地环境和气候适应方面可能发挥的关键作用。通过将泛基因组与转录组、甲基化组和染色质可及性图谱整合，我们揭示了泛基因和重复基因的进化轨迹与调控和表观遗传结构的局部基因组景观密切相关，特别是基因体区域的 CG 甲基化。进一步的比较基因组分析已经能够鉴定出跨物种的 142 202 个结构变异，这些变异与大量基因相交叉，并对表型和适应性分歧做出了重大贡献。我们通过实验验证了约 180 bp 的存在/不存在变异会影响该基因的表达，这对于叶片锯齿的形成至关重要。最后，我们开发了一个用户友好的基于网络的工具，包含与超级泛基因组相关的多组学资源（）。总之，目前林木中开创性的超级全基因组资源不仅有助于推进这一全球重要树属的育种工作，而且还为理解树木生物学的潜在途径提供了宝贵的见解。