Juglans (walnuts), the most speciose genus in the walnut family (Juglandaceae), represents most of the family's commercially valuable fruit and wood-producing trees. It includes several species used as rootstock for their resistance to various abiotic and biotic stressors. We present the full structural and functional genome annotations of six Juglans species and one outgroup within Juglandaceae (Juglans regia, J. cathayensis, J. hindsii, J. microcarpa, J. nigra, J. sigillata and Pterocarya stenoptera) produced using BRAKER2 semi-unsupervised gene prediction pipeline and additional tools. For each annotation, gene predictors were trained using 19 tissue-specific J. regia transcriptomes aligned to the genomes. Additional functional evidence and filters were applied to multi-exonic and mono-exonic putative genes to yield between 27 000 and 44 000 high-confidence gene models per species. Comparison of gene models to the BUSCO embryophyta dataset suggested that, on average, genome annotation completeness was 85.6%. We utilized these high-quality annotations to assess gene family evolution within Juglans, and among Juglans and selected Eurosid species. We found notable contractions in several gene families in J. hindsii, including disease resistance-related wall-associated kinase (WAK), Catharanthus roseus receptor-like kinase (CrRLK1L) and others involved in abiotic stress response. Finally, we confirmed an ancient whole-genome duplication that took place in a common ancestor of Juglandaceae using site substitution comparative analysis.

中文翻译：

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六个胡桃属物种的比较基因组学揭示了疾病相关的基因家族收缩。

胡桃（胡桃科）中最特殊的属核桃（胡桃科）代表了该家族大多数具有商业价值的水果和产木树。它包括几种用作砧木的种，因为它们对各种非生物和生物胁迫源具有抗性。我们介绍了使用BRAKER2半杂交技术生产的6个胡桃科物种和胡桃科（胡桃木，J. cathayensis，J.印度教，J. microcarpa，J. nigra，J. sigillata和Pterocarya stenoptera）中的6个Juglans物种和1个外群的完整结构和功能基因组注释。无监督的基因预测管道和其他工具。对于每个注释，使用与基因组对齐的19个组织特异性J. regia转录组训练基因预测因子。将其他功能证据和过滤器应用于多外显子和单外显子推定基因，以产生每个物种27 000至44 000个高置信度基因模型。基因模型与BUSCO胚胎植物数据集的比较表明，平均而言，基因组注释的完整性为85.6％。我们利用这些高质量的注释来评估核桃gla内，核桃gla和选定的欧洲s种之间的基因家族进化。我们在印度后裔中发现了几个基因家族的明显收缩，包括与疾病抗性相关的壁相关激酶（WAK），长春花玫瑰受体样激酶（CrRLK1L）和其他参与非生物胁迫反应的物种。最后，我们通过位点置换比较分析证实了在古猿科的共同祖先发生的古老的全基因组重复。