Satsuma mandarin (Citrus reticulata “Unshiu”) is a global cultivar with superior fruit characteristics and ranking among the top citrus cultivars in terms of production. It is also a key contributor to citrus breeding. However, the lack of high-quality genome makes the origin of Satsuma mandarin has long been a matter of debate. Here, we assembled a gap-free, high-quality genome of Satsuma mandarin. Meanwhile, we collected and sequenced 15 indigenous citrus varieties in Zhejiang Province, 12 Satsuma mandarins, 21 citrus hybrids related to Satsuma mandarin, 10 modern citrus varieties, and 7 other mandarins. Through high-resolution genome analysis, we inferred that Satsuma mandarin originated from a cross between C. reticulata “Ruju” × C. reticulata “Bendiguang” and proposed that Satsuma mandarin most probably originated in East area in Zhejiang Province of China, where the two parents-like cultivars are still found in a sympatric region to date. These results provide new insights into the origin model of Satsuma mandarin. The spread of mandarin is also discussed, which probably associated with the culture exchange and trade activities between Japan and China from Tang Dynasty and afterwards.

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