Garlic, an economically important vegetable, spice, and medicinal crop, produces highly enlarged bulbs and unique organosulfur compounds. Here, we report a chromosome-level genome assembly for garlic, with a total size of approximately 16.24 Gb, as well as the annotation of 57 561 predicted protein-coding genes, making garlic the first Allium species with a sequenced genome. Analysis of this garlic genome assembly reveals a recent burst of transposable elements, explaining the substantial expansion of the garlic genome. We examined the evolution of certain genes associated with the biosynthesis of allicin and inulin neoseries-type fructans, and provided new insights into the biosynthesis of these two compounds. Furthermore, a large-scale transcriptome was produced to characterize the expression patterns of garlic genes in different tissues and at various growth stages of enlarged bulbs. The reference genome and large-scale transcriptome data generated in this study provide valuable new resources for research on garlic biology and breeding.

大蒜是经济上重要的蔬菜，香料和药用作物，可产生高度膨大的鳞茎和独特的有机硫化合物。在这里，我们报告了大蒜的染色体级基因组装配，总大小约为16.24 Gb，并注释了57561个预测的蛋白质编码基因，使大蒜成为第一个葱属植物基因组测序的物种。对这种大蒜基因组装配的分析揭示了最近转座因子的爆发，解释了大蒜基因组的实质性扩展。我们检查了与大蒜素和菊粉新系列型果聚糖的生物合成相关的某些基因的进化，并为这两种化合物的生物合成提供了新见识。此外，产生了大规模的转录组以表征大蒜基因在不同组织中以及鳞茎的不同生长阶段的表达模式。本研究中产生的参考基因组和大规模转录组数据为大蒜生物学和育种研究提供了宝贵的新资源。