Paulownias are among the fastest growing trees in the world, but they often suffer tremendous loss of wood production due to infection by Paulownia witches' broom (PaWB) phytoplasmas. In this study, we have sequenced and assembled a high-quality nuclear genome of Paulownia fortunei, a commonly cultivated paulownia species. The assembled genome of P. fortunei is 511.6 Mb in size, with 93.2% of its sequences anchored to 20 pseudo-chromosomes, and it contains 31 985 protein-coding genes. Phylogenomic analyses show that the family Paulowniaceae is sister to a clade composed of Phrymaceae and Orobanchaceae. Higher photosynthetic efficiency is achieved by integrating C3 photosynthesis and the crassulacean acid metabolism pathway, which may contribute to the extremely fast growth habit of paulownia trees. Comparative transcriptome analyses reveal modules related to cambial growth and development, photosynthesis, and defense responses. Additional genome sequencing of PaWB phytoplasma, combined with functional analyses, indicates that the effector PaWB-SAP54 interacts directly with Paulownia PfSPLa, which in turn causes the degradation of PfSPLa by the ubiquitin-mediated pathway and leads to the formation of witches' broom. Taken together, these results provide significant insights into the biology of paulownias and the regulatory mechanism for the formation of PaWB.

泡桐是世界上生长最快的树木之一，但由于泡桐(PaWB) 植原体的感染，它们经常遭受巨大的木材产量损失。在这项研究中，我们对常见栽培泡桐物种泡桐的高质量核基因组进行了测序和组装。P. fortunei的组装基因组大小为 511.6 Mb，其 93.2% 的序列锚定在 20 条假染色体上，包含 31 985 个蛋白质编码基因。系统基因组分析表明，泡桐科是由 Phrymaceae 和 Orobanchaceae 组成的进化枝的姐妹。通过整合C3光合作用和景天酸代谢途径实现更高的光合效率，这可能有助于泡桐树极快的生长习性。比较转录组分析揭示了与形成层生长发育、光合作用和防御反应相关的模块。PaWB植原体的额外基因组测序，结合功能分析，表明效应器PaWB-SAP54直接与泡桐相互作用PfSPLa 反过来又通过泛素介导的途径导致 PfSPLa 的降解，并导致女巫扫帚的形成。总之，这些结果为泡桐生物学和 PaWB 形成的调控机制提供了重要的见解。