期刊
JOURNAL OF INTEGRATIVE PLANT BIOLOGY
卷 64, 期 8, 页码 1487-1501出版社
WILEY
DOI: 10.1111/jipb.13318
关键词
ancestral chromosome reconstruction; hawthorn (Crataegus spp; ); long terminal repeat retrotransposons (LTR-RTs); medicinal and edible plants; sub-genome
资金
- National Natural Science Foundation of China [32060237, 32060085]
- European Research Council (ERC) under the European Union's Horizon 2020 research and innovation program [833522]
- Ghent University (Methusalem) [BOF.MET.2021.0005.01]
In this study, we provide a new genome sequence of the hawthorn cultivar Qiu Jinxing and discover gene amplification in the flavonoid and triterpenoid biosynthetic pathways. We also explore the evolution of Maleae species and the paleo-polyploid origin patterns of Rosaceae. This research is of great importance for understanding the evolution of Maleae species and the horticultural improvement of hawthorn.
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.
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