Despite their economic importance and well-characterized domestication syndrome, the genomic impact of domestication and the identification of variants underlying the domestication traits in Cucurbita species (pumpkins and squashes) is currently lacking. Cucurbita argyrosperma, also known as cushaw pumpkin or silver-seed gourd, is a Mexican crop consumed primarily for its seeds rather than fruit flesh. This makes it a good model to study Cucurbita domestication, as seeds were an essential component of early Mesoamerican diet and likely the first targets of human-guided selection in pumpkins and squashes. We obtained population-level data using tunable Genotype by Sequencing libraries for 192 individuals of the wild and domesticated subspecies of C. argyrosperma across Mexico. We also assembled the first wild Cucurbita genome at a chromosome level. Comparative genomic analyses revealed several structural variants and presence/absence of genes related to domestication. Our results indicate a monophyletic origin of this domesticated crop in the lowlands of Jalisco. We uncovered candidate domestication genes that are involved in the synthesis and regulation of growth hormones, plant defense mechanisms, flowering time and seed development. The presence of shared selected alleles with the closely related species Cucurbita moschata suggests domestication-related introgression between both taxa.

中文翻译：

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野生南瓜基因组揭示了结构变异和基因渗入在驯化中的作用

尽管它们具有经济重要性和特征明确的驯化综合症，但目前缺乏葫芦科物种（南瓜和南瓜）的驯化的基因组影响以及对驯化性状潜在变异的识别。西葫芦（Cucurbita argyrosperma），又称南瓜南瓜或银瓜，是一种墨西哥农作物，主要用于种子而不是果肉。这使它成为研究南瓜属驯化的一个很好的模型，因为种子是中美洲早期饮食中不可或缺的组成部分，并且可能是南瓜和南瓜中人类指导选择的第一个目标。我们通过测序文库获得了192个野生和驯化亚种的种群的可调谐基因型，从而获得了种群水平的数据。墨西哥各地的C. argyrosperma。我们还在染色体水平上组装了第一个野生南瓜属基因组。比较基因组分析揭示了几种结构变异以及与驯化有关的基因的存在/不存在。我们的结果表明，这种驯化作物在哈利斯科州的低地具有单系起源。我们发现了候选驯化基因，这些基因与生长激素的合成和调控，植物防御机制，开花时间和种子发育有关。与密切相关的南瓜属物种Cucurbita moschata共有选定的等位基因，表明这两个分类单元之间都有驯化相关的基因渗入。