Rubus rosaefolius is a kind of red raspberry possessing high nutritional and pharmaceutical value. Here, we present a chromosome-level draft genome of R. rosaefolius. Of the total 131 assembled scaffolds, 70 with a total size of 219.02 Mb, accounting for 99.33% of the estimated genome size, were anchored to seven pseudochromosomes. We traced a whole-genome duplication (WGD) event shared among members of the Rosaceae family, which derived 5090 currently detectable duplicated gene pairs (dgps). 75.09% of the WGD-dgps underwent purifying selection, and approximately three-quarters of informative WGD-dgps expressed their two paralogs with significant differences. We detected a wide variety of anthocyanins in the berries of R. rosaefolius, and their total concentration remained relatively stable during berry development but increased rapidly during the ripening stage, mainly because of the contributions of pelargonidin-3-O-glucoside and pelargonidin-3-O-(6”-O-malonyl)glucoside. We identified many structural genes that encode enzymes, such as RrDFR, RrF3H, RrANS, and RrBZ1, and play key roles in anthocyanin biosynthesis. The expression of some of these genes significantly increased or decreased with the accumulation of pelargonidin-3-O-glucoside and pelargonidin-3-O-(6”-O-malonyl)glucoside. We also identified some transcription factors and specific methylase-encoding genes that may play a role in regulating anthocyanin biosynthesis by targeting structural genes. In conclusion, our findings provide deeper insights into the genomic evolution and molecular mechanisms underlying anthocyanin biosynthesis in berry of R. rosaefolius. This knowledge may significantly contribute to the targeted domestication and breeding of Rubus species.

中文翻译：

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染色体规模的基因组以及转录组和代谢组为了解悬钩子（Rubus rosaefolius Sm）的进化和花青素生物合成提供了见解。（蔷薇科）

悬钩子（Rubus rosaefolius）是一种具有很高营养和药用价值的红树莓。在这里，我们提出了 R. rosaefolius 的染色体水平基因组草图。在总共 131 个组装的支架中，有 70 个总大小为 219.02 Mb，占估计基因组大小的 99.33%，固定在 7 个假染色体上。我们追踪了蔷薇科成员之间共享的全基因组重复 (WGD) 事件，该事件衍生出 5090 个目前可检测到的重复基因对 (dgps)。75.09% 的 WGD-dgps 经历了纯化选择，大约四分之三的信息丰富的 WGD-dgps 表达了两个具有显着差异的旁系同源物。我们在玫瑰花的浆果中检测到多种花青素，其总浓度在浆果发育过程中保持相对稳定，但在成熟阶段迅速增加，这主要是天竺葵素-3-O-葡萄糖苷和天竺葵素-3的贡献。 -O-(6”-O-丙二酰基)葡萄糖苷。我们鉴定了许多编码酶的结构基因，例如 RrDFR、RrF3H、RrANS 和 RrBZ1，并在花青素生物合成中发挥关键作用。其中一些基因的表达随着天竺葵素-3-O-葡萄糖苷和天竺葵素-3-O-(6”-O-丙二酰基)葡萄糖苷的积累而显着增加或减少。我们还鉴定了一些转录因子和特定甲基化酶编码基因，它们可能通过靶向结构基因在调节花青素生物合成中发挥作用。总之，我们的研究结果为玫瑰果浆果中花青素生物合成的基因组进化和分子机制提供了更深入的见解。这些知识可能会对悬钩子属物种的有针对性的驯化和育种做出重大贡献。