Rosa, a genus esteemed worldwide for its ornamental plants, has encountered barriers in functional genomic studies and further genetic enhancement due to incomplete sequences and floating regions in previously sequenced genomes. Our groundbreaking study introduced a meticulously assembled, continuous, and fully bridged reference genome for Rosa rugosa, constructed through a sophisticated combination of PacBio High-Fidelity, ONT ultra-long reads, and Hi-C data. This robust assembly spanned 444.55 Mb and encompassed 34 109 protein-coding genes. We have uniquely assembled each chromosome into single, gap-free structures, successfully identifying all 14 telomeres and seven centromeres, a feat not achieved previously. The centromeric regions were distinguished by tandem repeats, primarily composed of centromere-specific 159-bp monomers, and a significant enrichment of ATHILA/Gypsy long terminal repeat retrotransposons in proximal regions. Our research highlighted recent tandem duplications as instrumental in bolstering R. rugosa's stress tolerance, environmental adaptability, and enhanced anthocyanin synthesis. Furthermore, our study ventured into uncharted territory by predicting transcription factors potentially regulating anthocyanin biosynthesis through the employment of gene co-expression networks, providing new avenues for research. This comprehensive reference genome not only serves as a cornerstone for in-depth exploration of genomic architecture and functionalities in R. rugosa but also acts as a catalyst for innovative breeding strategies and genetic refinement within the genus.

中文翻译：

---

玫瑰参考基因组的端粒到端粒的无间隙组装


蔷薇属因其观赏植物而在世界范围内享有盛誉，但由于先前测序的基因组中的不完整序列和浮动区域，在功能基因组研究和进一步遗传增强方面遇到了障碍。我们的开创性研究引入了精心组装、连续且完全桥接的玫瑰参考基因组，该参考基因组是通过 PacBio 高保真度、ONT 超长读取和 Hi-C 数据的复杂组合构建的。这个强大的组装跨越 444.55 Mb，包含 34 109 个蛋白质编码基因。我们以独特的方式将每条染色体组装成单个无间隙结构，成功识别出所有 14 个端粒和 7 个着丝粒，这是以前从未实现过的壮举。着丝粒区域的特征是串联重复序列，主要由着丝粒特异性的 159 bp 单体组成，并且近端区域显着富集 ATHILA/Gypsy 长末端重复反转录转座子。我们的研究强调了最近的串联复制有助于增强 R. rugosa 的应激耐受性、环境适应性和增强花青素合成。此外，我们的研究通过利用基因共表达网络预测可能调节花青素生物合成的转录因子，进入了未知领域，为研究提供了新途径。这个全面的参考基因组不仅可以作为深入探索红花基因组结构和功能的基石，而且可以作为该属内创新育种策略和遗传改良的催化剂。