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Paleo-polyploidization in Lycophytes

Genomics, Proteomics & Bioinformatics 2020年第3期18卷 333-340页

作者： Jinpeng Wang Jigao Yu Pengchuan sun Chao Li Xiaoming Song Tianyu Lei Yuxian Li Jiaqing Yuan sangrong sun Hongling Ding Xueqian Duan Shaoqi Shen Yanshuang Shen Jing Li Fanbo Meng Yangqin Xie Jianyu Wang Yue Hou Jin Zhang Xianchun Zhang Xiu-Qing Li Andrew HPaterson Xiyin Wang Center for Computational Biology and Genomics and School of Life SciencesNorth China University of Science and TechnologyTangshan 063200China National Key Laboratory for North China Crop Improvement and Regulation Agriculture University of HebeiBaoding 071001China State Key Laboratory of Systematic and Evolutionary Botany Institute of BotanyChinese Academy of ScienceBeijing 100093China Fredericton Research and Development Centre Agriculture and Agri-Food CanadaFrederictonNew BrunswickE3B 4Z7Canada Plant Genome Mapping Laboratory University of AthensAthensGA 30602USA Department of Plant Biology University of GeorgiaAthensGA 30602USA Department of Crop and Soil Science University of GeorgiaAthensGA 30602USA Department of Genetics University of GeorgiaAthensGA 30602USA

Lycophytes and seed plants constitute the typical vascular *** have been thought to have no paleo-polyploidization although the event is known to be critical for the fast expansion of seed ***,genomic analyses including the homologous gene dot plot analysis detected multiple paleo-polyploidization events,with one occurring approximately 13–15 million years ago(MYA)and another about 125–142 MYA,during the evolution of the genome of Selaginella moellendorffii,a model *** addition,comparative analysis of reconstructed ancestral genomes of lycophytes and angiosperms suggested that lycophytes were affected by more paleopolyploidization events than seed *** from the present genomic analyses indicate that paleo-polyploidization has contributed to the successful establishment of both lineages—lycophytes and seed plants—of vascular plants.

关键词： Vascular plant Lycophytes Genome Polyploidy Evolution

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

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Horticultural Plant Journal 2023年第2期9卷 306-320页

作者： Jianyu Wang Ziyi Yang Tianyu Lei Yan Zhang Qimeng Xiao Zijian Yu Jiaqi Zhang sangrong sun Qiang Xu Shaoqi Shen Zimo Yan Mengnan Fang Yue Ding Zihan Liu Qianwen Zhu Ke Ren Yuxin Pan Haibin Liu Jinpeng Wang School of Life Sciences Center for Genomics and Computational BiologyNorth China University of Science and TechnologyTangshanHebei 063000China State Key Laboratory of Systematic and Evolutionary Botany Institute of BotanyChinese Academy of ScienceBeijing 100093China University of Chinese Academy of Sciences Beijing 100049China

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 *** 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 7chromosomal fusions that have shaped the T. sinensis genome;more information is available on a newly constructed karyotype platform(http://***/Toona_sinensis/***). 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.

关键词： Toona sinensis Alignment Autotetraploidization Karyotype evolution Terpene synthase genes

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