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Research paper

A likely autotetraploidization event shaped the Chinese mahogany (Toona sinensis) genome

Jianyu Wanga,1Ziyi Yanga,1Tianyu Leia,1Yan ZhangaQimeng XiaoaZijian YuaJiaqi ZhangaSangrong SunaQiang XuaShaoqi ShenaZimo YanaMengnan FangaYue DingaZihan LiuaQianwen ZhuaKe RenaYuxin Pana( )Haibin Liua( )Jinpeng Wanga,b,c( )
School of Life Sciences, Center for Genomics and Computational Biology, North China University of Science and Technology, Tangshan, Hebei 063000, China
State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Science, Beijing 100093, China
University of Chinese Academy of Sciences, Beijing 100049, China

1 These authors contributed equally to this work.

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Abstract

Chinese mahogany (Toona sinensis) is of considerable medical and economic importance, and its genome has been deciphered. However, the process underlying its polyploidy is unclear, and the chromosomal evolutionary trajectory is poorly understood. Here, by reanalysing the T. sinensis genome, we found evidence of a tetraploidization event (T. sinensis special tetraploidization, TST) that occurred approximately 15–17 million years ago (MYA) after the core eudicot-common hexaploidization (ECH or gamma) event. We characterized the synonymous nucleotide substitution rates (Ks values) of collinear genes and found that T. sinensis genes affected by the TST evolve at a slower rate than Acer yangbiense genes. Furthermore, we identified homologous genes related to polyploidization and speciation and constructed multiple alignments with different reference genomes. Notably, the significant balance of gene retention and loss characterized in the two TST-derived subgenomes suggests an autopolyploid nature of the TST. Moreover, we deduced the chromosomal karyotypes of the two subgenomes and identified 7 chromosomal fusions that have shaped the T. sinensis genome; more information is available on a newly constructed karyotype platform (http://www.cgrpoee.top/Toona_sinensis/index.html). The T. sinensis genome preserves the ancestral chromosome structure of dicotyledons well and could serve as a good reference for understanding genomic changes in other Meliaceae and Sapindales plants. In addition, we verified that tandem duplication and the ECH have promoted the expansion of terpene synthase (TPS) genes; conversely, the TST seems to have inhibited expansion of these genes. This present effort has clarified the polyploidy events of the T. sinensis genome, filled gaps in the history of karyotype evolution, and laid a solid foundation for further genomic studies in the Meliaceae research community and beyond.

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Horticultural Plant Journal
Pages 306-320
Cite this article:
Wang J, Yang Z, Lei T, et al. A likely autotetraploidization event shaped the Chinese mahogany (Toona sinensis) genome. Horticultural Plant Journal, 2023, 9(2): 306-320. https://doi.org/10.1016/j.hpj.2022.11.002

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Received: 08 April 2022
Revised: 15 June 2022
Accepted: 09 September 2022
Published: 09 November 2022
© 2022 Chinese Society for Horticultural Science (CSHS) and Institute of Vegetables and Flowers (IVF), Chinese Academy of Agricultural Sciences (CAAS).

This is an open access article under the CC BY-NC-ND license (http://creativecommons.org/licenses/by-nc-nd/4.0/).

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