Genomic insights into the evolutionary history and conservation of the living fossil Tetracentron sinense

doi:10.1016/j.pld.2025.05.008

Plant Diversity ›› 2025, Vol. 47 ›› Issue (05): 759-771.DOI: 10.1016/j.pld.2025.05.008

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Genomic insights into the evolutionary history and conservation of the living fossil Tetracentron sinense

Zhao-Yang Jing (景昭阳)^a,b, Ren-Gang Zhang (张仁纲)^c,d, Yang Liu (刘阳)^c,d, Ke-Guang Cheng (程可光)^a,b, De-Tuan Liu (刘德团)^c,d, Heng Shu (舒恒)^c,d, Jiali Kong (孔佳莉)^e, Zhong-Hua Liu (刘忠华)^a,b, Yong-Peng Ma (马永鹏)^c,d, Ping-Li Liu (刘平丽)^a,b

a. State Key Laboratory of Tree Genetics and Breeding, National Engineering Research Center of Tree Breeding and Ecological Restoration, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, College of Biological Sciences and Technology, Beijing Forestry University, Beijing 100083, China;
b. Institute of Tree Development and Genome Editing, Beijing Forestry University, Beijing 100083, China;
c. Yunnan Key Laboratory for Integrative Conservation of Plant Species with Extremely Small Populations, State Key Laboratory of Plant Diversity and Specialty Crops, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China;
d. University of the Chinese Academy of Sciences, Beijing 100049, China;
e. Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Synthetic Biology, Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China

Received:2024-10-09 Revised:2025-05-19 Online:2025-09-29 Published:2025-09-29
Contact: Ping-Li Liu,E-mail:liupl@bjfu.edu.cn
Supported by:
We thank Wen-Hua Yang for technical assistance. This work was supported by the National Natural Science Foundation of China (no. 32570426), the Key Basic Research Program of Yunnan Province, China (202101BC070003), the Fundamental Research Funds for the Central Universities (QNTD202502), and the STI 2030—Major Program (2022ZD0401605-2).

Genomic insights into the evolutionary history and conservation of the living fossil Tetracentron sinense

a. State Key Laboratory of Tree Genetics and Breeding, National Engineering Research Center of Tree Breeding and Ecological Restoration, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, College of Biological Sciences and Technology, Beijing Forestry University, Beijing 100083, China;
b. Institute of Tree Development and Genome Editing, Beijing Forestry University, Beijing 100083, China;
c. Yunnan Key Laboratory for Integrative Conservation of Plant Species with Extremely Small Populations, State Key Laboratory of Plant Diversity and Specialty Crops, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China;
d. University of the Chinese Academy of Sciences, Beijing 100049, China;
e. Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Synthetic Biology, Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China

通讯作者: Ping-Li Liu,E-mail:liupl@bjfu.edu.cn
基金资助:
We thank Wen-Hua Yang for technical assistance. This work was supported by the National Natural Science Foundation of China (no. 32570426), the Key Basic Research Program of Yunnan Province, China (202101BC070003), the Fundamental Research Funds for the Central Universities (QNTD202502), and the STI 2030—Major Program (2022ZD0401605-2).

Abstract

Abstract: Tetracentron sinense is a 'living fossil' tree in East Asia. Understanding how this 'living fossil' responds to climate change and adapts to local environments is critical for its conservation. Here, we used re-sequenced genomes to clarify the evolutionary history and adaptive potential of T. sinense. We identified six divergent lineages in T. sinense: three lineages from southwestern China (Yunnan Province) and three lineages from the central subtropical region of China. Additionally, we detected hybridization events between some adjacent lineages. Demographic analysis revealed that over the past 10,000 years the effective population size (Ne) of three T. sinense lineages (i.e., NORTH, SWEST, and YNWEST) increased after their last bottleneck and then remained stable, whereas that of the remaining three lineages (i.e., YSEAST, YC, and EAST) declined steadily. The decline in effective population size in the Yunnan lineages aligned well with the decrease in genome-wide diversity and a significant increase in the frequency of runs of homozygosity. Deleterious variants and positively selected sites were involved in the evolution of different lineages. Further, genotype–environment association (GEA) analyses indicated adaptation to temperature- and precipitation-related factors. Genomic offset analyses found the most vulnerable populations, while SC and SC-yad were predicted to better handle extreme changes. Our findings provide insights into the evolutionary history and conservation of T. sinense and enhance our understanding of the evolution of living fossil species.

Key words: Tetracentron sinense, Hybridization, Deleterious mutation, Local adaptation, Genomic vulnerability

摘要： Tetracentron sinense is a 'living fossil' tree in East Asia. Understanding how this 'living fossil' responds to climate change and adapts to local environments is critical for its conservation. Here, we used re-sequenced genomes to clarify the evolutionary history and adaptive potential of T. sinense. We identified six divergent lineages in T. sinense: three lineages from southwestern China (Yunnan Province) and three lineages from the central subtropical region of China. Additionally, we detected hybridization events between some adjacent lineages. Demographic analysis revealed that over the past 10,000 years the effective population size (Ne) of three T. sinense lineages (i.e., NORTH, SWEST, and YNWEST) increased after their last bottleneck and then remained stable, whereas that of the remaining three lineages (i.e., YSEAST, YC, and EAST) declined steadily. The decline in effective population size in the Yunnan lineages aligned well with the decrease in genome-wide diversity and a significant increase in the frequency of runs of homozygosity. Deleterious variants and positively selected sites were involved in the evolution of different lineages. Further, genotype–environment association (GEA) analyses indicated adaptation to temperature- and precipitation-related factors. Genomic offset analyses found the most vulnerable populations, while SC and SC-yad were predicted to better handle extreme changes. Our findings provide insights into the evolutionary history and conservation of T. sinense and enhance our understanding of the evolution of living fossil species.

关键词: Tetracentron sinense, Hybridization, Deleterious mutation, Local adaptation, Genomic vulnerability

Zhao-Yang Jing (景昭阳), Ren-Gang Zhang (张仁纲), Yang Liu (刘阳), Ke-Guang Cheng (程可光), De-Tuan Liu (刘德团), Heng Shu (舒恒), Jiali Kong (孔佳莉), Zhong-Hua Liu (刘忠华), Yong-Peng Ma (马永鹏), Ping-Li Liu (刘平丽). Genomic insights into the evolutionary history and conservation of the living fossil Tetracentron sinense[J]. Plant Diversity, 2025, 47(05): 759-771.

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Genomic insights into the evolutionary history and conservation of the living fossil Tetracentron sinense

Genomic insights into the evolutionary history and conservation of the living fossil Tetracentron sinense

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