Most molecularly characterized plant resistance genes (R genes) belong to the nucleotide-binding-site-leucine-rich-repeat (NLR) receptor family and are prone to duplication and transposition with high sequence diversity. In this family, theVatgene in melon is one of the few R genes known for conferring resistance to insect, i.e.,Aphis gossypii, but it has been misassembled and/or mispredicted in the whole genomes of Cucurbits. We examined 14 genomic regions (about 400 kb) derived from long-read assemblies spanningVat-related genes inCucumis melo,Cucumis sativus, Citrullus lanatus, Benincasa hispida, Cucurbita argyrosperma, andMomordica charantia. We built the phylogeny of those genes. Investigating the paleohistory of theVatgene cluster, we revealed a step by step process beginning from a common ancestry in cucurbits older than 50 my. We highlightedVatexclusively in theCucumisgenera, which diverged about 20 my ago. We then focused on melon, evaluating a minimum duplication rate ofVatin 80 wild and cultivated melon lines using generalist primers; our results suggested that duplication started before melon domestication. The phylogeny of 44 Vat-CDS obtained from 21 melon lines revealed gain and loss of leucine-rich-repeat domains along diversification. Altogether, we revealed the high putative recognition scale offered in melon based on a combination of SNPs, number of leucine-rich-repeat domains within each homolog and number of homologs within each cluster that might jointly confer resistance to a large pest and pathogen spectrum. Based on our findings, we propose possible avenues for breeding programs.

中文翻译：

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构建一组赋予对害虫和病原体抗性的 NLR 基因：葫芦中 Vat 基因簇的故事

大多数分子特征的植物抗性基因（R基因）属于核苷酸结合位点富含亮氨酸的重复（NLR）受体家族，并且易于复制和转座，具有高度的序列多样性。在这个家庭中，增值税甜瓜中的基因是少数已知的赋予昆虫抗性的 R 基因之一，即棉蚜, 但它在葫芦科植物的整个基因组中被错误组装和/或错误预测。我们检查了 14 个基因组区域（约 400 kb），这些区域来自于跨越的长读长组装增值税相关基因甜瓜,Cucumis sativus, Citrullus lanatus, Benincasa hispida, Cucurbita argyrosperma， 和苦瓜. 我们建立了这些基因的系统发育。调查古史增值税基因簇，我们揭示了从 50 岁以上葫芦科植物的共同祖先开始的逐步过程。我们强调了增值税专门在黄瓜属，大约在我 20 年前分道扬镳。然后我们专注于甜瓜，评估最小重复率增值税使用通用引物在 80 个野生和栽培甜瓜品系中；我们的结果表明，复制在甜瓜驯化之前就开始了。从 21 个甜瓜品系获得的 44 个 Vat-CDS 的系统发育揭示了富含亮氨酸的重复结构域随着多样化的增加和减少。总而言之，我们揭示了基于 SNP、每个同源物中富含亮氨酸的重复结构域的数量和每个簇中的同源物数量的组合在甜瓜中提供的高推定识别规模，这可能共同赋予对大型害虫和病原体谱的抗性。根据我们的发现，我们提出了育种计划的可能途径。