Two-step model of paleohexaploidy, ancestral genome reshuffling and plasticity of heat shock response in Asteraceae

Abstract

An ancient hexaploidization event in the most but not all Asteraceae plants, may have been responsible for shaping the genomes of many horticultural, ornamental, and medicinal plants that promoting the prosperity of the largest angiosperm family on the earth. However, the duplication process of this hexaploidy, as well as the genomic and phenotypic diversity of extant Asteraceae plants caused by paleogenome reorganization, are still poorly understood. We analyzed 11 genomes from 10 genera in Asteraceae, and redated the Asteraceae common hexaploidization (ACH) event ∼70.7–78.6 million years ago (Mya) and the Asteroideae specific tetraploidization (AST) event ∼41.6–46.2 Mya. Moreover, we identified the genomic homologies generated from the ACH, AST and speciation events, and constructed a multiple genome alignment framework for Asteraceae. Subsequently, we revealed biased fractionations between the paleopolyploidization produced subgenomes, suggesting the ACH and AST both are allopolyplodization events. Interestingly, the paleochromosome reshuffling traces provided clear evidence for the two-step duplications of ACH event in Asteraceae. Furthermore, we reconstructed ancestral Asteraceae karyotype (AAK) that has 9 paleochromosomes, and revealed a highly flexible reshuffling of Asteraceae paleogenome. Of specific significance, we explored the genetic diversity of Heat Shock Transcription Factors ( Hsfs) associated with recursive whole-genome polyploidizations, gene duplications, and paleogenome reshuffling, and revealed that the expansion of Hsfs gene families enable heat shock plasticity during the genome evolution of Asteraceae. Our study provides insights on polyploidy and paleogenome remodeling for the successful establishment of Asteraceae, and is helpful for further communication and exploration of the diversification of plant families and phenotypes.

Acknowledgements

This work was funded by the National Natural Science Foundation of China (32170236 and 31501333 to J.P.W.), the Hebei Natural Science Foundation (C2020209064 to J.P.W.), and the Fundamental Research for the Hebei Province Universities (JQN2020018 to T.L.).

Authors contributions

J.P.W. conceived the project and was responsible for the project initiation. J.P.W., X.K., C.X., and T.L. supervised and managed the project and research. Z.W., S.B., Y.F., J.Q.W., Z.Y., F.L., Z.X., Y.H., X.G., Y.L., Y.D. and J.Y.W. performed the analysis. The manuscript was organized, written and revised by J.P.W., X.K., Y.Z., All authors read and approved the manuscript.

Data availability

All original data in this study are available through the article /Supplementary Material.

Conflict of interest statement

The authors declare no conflicts of interest.

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