College of Chinese Material Medica, Yunnan University of Chinese Medicine, Kunming, 650500, China.
School of Agriculture, Yunnan University, Kunming, 650091, China.
J Integr Plant Biol. 2022 Aug;64(8):1487-1501. doi: 10.1111/jipb.13318. Epub 2022 Jul 25.
Cultivated hawthorn (Crataegus pinnatifida var. major) is an important medicinal and edible plant with a long history of use for health protection in China. Herein, we provide a de novo chromosome-level genome sequence of the hawthorn cultivar "Qiu Jinxing." We assembled an 823.41 Mb genome encoding 40 571 genes and further anchored the 779.24 Mb sequence into 17 pseudo-chromosomes, which account for 94.64% of the assembled genome. Phylogenomic analyses revealed that cultivated hawthorn diverged from other species within the Maleae (apple tribe) at approximately 35.4 Mya. Notably, genes involved in the flavonoid and triterpenoid biosynthetic pathways have been significantly amplified in the hawthorn genome. In addition, our results indicated that the Maleae share a unique ancient tetraploidization event; however, no recent independent whole-genome duplication event was specifically detected in hawthorn. The amplification of non-specific long terminal repeat retrotransposons contributed the most to the expansion of the hawthorn genome. Furthermore, we identified two paleo-sub-genomes in extant species of Maleae and found that these two sub-genomes showed different rearrangement mechanisms. We also reconstructed the ancestral chromosomes of Rosaceae and discussed two possible paleo-polyploid origin patterns (autopolyploidization or allopolyploidization) of Maleae. Overall, our study provides an improved context for understanding the evolution of Maleae species, and this new high-quality reference genome provides a useful resource for the horticultural improvement of hawthorn.
培育山楂（Crataegus pinnatifida var. major）是一种重要的药用和食用植物，在中国有着悠久的保健历史。在此，我们提供了山楂品种“秋金星”的从头染色体水平基因组序列。我们组装了一个 823.41 Mb 的基因组，编码 40571 个基因，并将 779.24 Mb 的序列进一步锚定到 17 条假染色体上，占组装基因组的 94.64%。系统发育分析表明，栽培山楂与苹果族（Maleae）中的其他物种在大约 3540 万年前分化。值得注意的是，在山楂基因组中，黄酮类和三萜类生物合成途径的基因显著扩增。此外，我们的研究结果表明，Maleae 具有独特的古老四倍体化事件；然而，在山楂中并未发现特定的近期独立全基因组复制事件。非特异性长末端重复反转录转座子的扩增对山楂基因组的扩张贡献最大。此外，我们在现存的 Maleae 物种中鉴定出两个古亚基因组，并发现这两个亚基因组表现出不同的重排机制。我们还重建了蔷薇科的祖先染色体，并讨论了 Maleae 的两种可能的古多倍体起源模式（自多倍体化或异源多倍体化）。总的来说，我们的研究为理解 Maleae 物种的进化提供了一个改进的背景，这个新的高质量参考基因组为山楂的园艺改良提供了一个有用的资源。
