Cultivated hawthorn (Crataegus pinnatifida var. major) genome sheds light on the evolution of Maleae (apple tribe)
Crabbe, M. James C.
Van de Peer, Yves
Crataegus pinnatifida var. major
ancestral chromosome reconstruction
hawthorn (Crataegus spp.)
long terminal repeat retrotransposons (LTR-RTs)
medicinal and edible plants
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AbstractCultivated 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.
CitationZhang T, Qiao Q, Du X, Zhang X, Hou Y, Wei X, Sun C, Zhang R, Yun Q, Crabbe MJC, Van de Peer Y, Dong W (2022) 'Cultivated hawthorn (Crataegus pinnatifida var. major) genome sheds light on the evolution of Maleae (apple tribe)', Journal of Integrative Plant Biology, 64 (8), pp.1487-1501.
SponsorsThis work is supported by grants from National Natural Science Foundation of China (32060237 to T.Z. and 32060085 to Q.Q.). YVdP acknowledges funding from the European Research Council (ERC) under the European Union's Horizon 2020 research and innovation program (No. 833522) and from Ghent University (Methusalem funding, BOF. MET.2021.0005.01).
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