Ginkgo biloba, the last extant representative of a lineage of Mesozoic gymnosperms, is one of the few seed plants with an exceptionally long (~300 Myr) evolutionary history free of genome-wide duplications (polyploidy). Despite this genome conservatism, we have recently found a viable spontaneous tetraploid Ginkgo sapling during routine screening of several plants, demonstrating that natural polyploidy is possible in Ginkgo. Here we provide a much wider flow cytometry survey of ploidy in some European Ginkgo collections, and own seedlings (>2200 individuals and ~200 cultivars). We found a surprisingly high level of ploidy variation in modern-day Ginkgo and documented altogether 13 haploid, 3 triploid, and 10 tetraploid Ginkgo plants or cultivars, most of them being morphologically distinct from common diploids. Haploids frequently produced polyploid (dihaploid) buds or branches. Tetraploids showed some genome size variation. The surveyed plants provide a unique resource for future Ginkgo research and breeding, and they might be used to accelerate the modern diversification of this nearly extinct plant lineage.

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