BACKGROUND The release of the first reference genome of walnut (Juglans regia L.) enabled many achievements in the characterization of walnut genetic and functional variation. However, it is highly fragmented, preventing the integration of genetic, transcriptomic, and proteomic information to fully elucidate walnut biological processes. FINDINGS Here, we report the new chromosome-scale assembly of the walnut reference genome (Chandler v2.0) obtained by combining Oxford Nanopore long-read sequencing with chromosome conformation capture (Hi-C) technology. Relative to the previous reference genome, the new assembly features an 84.4-fold increase in N50 size, with the 16 chromosomal pseudomolecules assembled and representing 95% of its total length. Using full-length transcripts from single-molecule real-time sequencing, we predicted 37,554 gene models, with a mean gene length higher than the previous gene annotations. Most of the new protein-coding genes (90%) present both start and stop codons, which represents a significant improvement compared with Chandler v1.0 (only 48%). We then tested the potential impact of the new chromosome-level genome on different areas of walnut research. By studying the proteome changes occurring during male flower development, we observed that the virtual proteome obtained from Chandler v2.0 presents fewer artifacts than the previous reference genome, enabling the identification of a new potential pollen allergen in walnut. Also, the new chromosome-scale genome facilitates in-depth studies of intraspecies genetic diversity by revealing previously undetected autozygous regions in Chandler, likely resulting from inbreeding, and 195 genomic regions highly differentiated between Western and Eastern walnut cultivars. CONCLUSION Overall, Chandler v2.0 will serve as a valuable resource to better understand and explore walnut biology.

中文翻译：

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核桃 (Juglans regia L.) 参考基因组的高质量染色体规模组装。

背景技术第一个核桃（Juglans regia L.）参考基因组的发布使核桃遗传和功能变异表征取得了许多成果。然而，它高度碎片化，阻碍了遗传、转录组和蛋白质组信息的整合，无法充分阐明核桃的生物学过程。在此，我们报告了通过将牛津纳米孔长读长测序与染色体构象捕获（Hi-C）技术相结合而获得的核桃参考基因组（Chandler v2.0）的新染色体规模组装。相对于之前的参考基因组，新组装的N50大小增加了84.4倍，组装了16个染色体假分子，占其总长度的95%。利用单分子实时测序的全长转录本，我们预测了 37,554 个基因模型，平均基因长度高于之前的基因注释。大多数新的蛋白质编码基因（90%）都存在起始密码子和终止密码子，这与 Chandler v1.0（仅 48%）相比有了显着的改进。然后我们测试了新的染色体水平基因组对核桃研究不同领域的潜在影响。通过研究雄花发育过程中发生的蛋白质组变化，我们观察到从 Chandler v2.0 获得的虚拟蛋白质组比之前的参考基因组呈现更少的伪影，从而能够识别核桃中新的潜在花粉过敏原。此外，新的染色体规模基因组通过揭示 Chandler 中以前未检测到的自合区域（可能是近交造成的）以及西方和东方核桃品种之间高度差异的 195 个基因组区域，促进了对种内遗传多样性的深入研究。结论 总的来说，Chandler v2.0 将成为更好地理解和探索核桃生物学的宝贵资源。