Horticulture Research

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Article|11 Apr 2024|OPEN

Efficient purging of deleterious mutations contributes to the survival of a rare conifer

Yi Wang¹ ^,† , Yongzhi Yang² ^,† , Zhitong Han¹ ^,† , Jialiang Li¹ ^,† , Jian Luo³ ^,† , Heng Yang¹ , Jingge Kuang¹ , Dayu Wu¹ , Shiyang Wang¹ , Sonam Tso⁴ , Tsam Ju⁴ , Jianquan Liu¹ ^, , Susanne S. Renner⁵ ^, and Mao Kangshan,^1,4 ^,

¹Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, Sichuan Zoige Alpine Wetland Ecosystem National Observation and Research Station, College of Life Sciences, State Key Laboratory of Hydraulics and Mountain River Engineering, Sichuan University, Chengdu 610065, China
²State Key Laboratory of Herbage Improvement and Grassland Agro-ecosystems, College of Ecology, Lanzhou University, Lanzhou 730000, China
³Xizang Key Laboratory of Forest Ecology in Plateau Area of Ministry of Education, National Key Station of Field Scientific Observation & Experiment of Alpine Forest Ecology System in Nyingchi, Research Institute of Xizang Plateau Ecology, Xizang Agriculture & Animal Husbandry University, Nyingchi 860000, China
⁴School of Ecology and Environment, Tibet University, Lhasa 850000, China
⁵Department of Biology, Washington University, Saint Louis, MO 63130, USA
*Corresponding author. E-mail: liujq@nwipb.ac.cn,srenner@wustl.edu,maokangshan@scu.edu.cn
^†Yi Wang,Yongzhi Yang,Zhitong Han,Jialiang Li and Jian Luo contributed equally to the study.

Horticulture Research 11,
Article number: uhae108 (2024)
doi: https://doi.org/10.1093/hr/uhae108
Views: 1307

Received: 30 Jan 2024
Accepted: 01 Apr 2024
Published online: 11 Apr 2024

Abstract

Cupressaceae is a conifer family rich in plants of horticultural importance, including Cupressus, Chamaecyparis, Juniperus, and Thuja, yet genomic surveys are lacking for this family. Cupressus gigantea, one of the many rare conifers that are threatened by climate change and anthropogenic habitat fragmentation, plays an ever-increasing role in ecotourism in Tibet. To infer how past climate change has shaped the population evolution of this species, we generated a de novo chromosome-scale genome (10.92 Gb) and compared the species’ population history and genetic load with that of a widespread close relative, C. duclouxiana. Our demographic analyses, based on 83 re-sequenced individuals from multiple populations of the two species, revealed a sharp decline of population sizes during the first part of the Quaternary. However, populations of C. duclouxiana then started to recover, while C. gigantea populations continued to decrease until recently. The total genomic diversity of C. gigantea is smaller than that of C. duclouxiana, but contrary to expectations, C. gigantea has fewer highly and mildly deleterious mutations than C. duclouxiana, and simulations and statistical tests support purifying selection during prolonged inbreeding as the explanation. Our results highlight the evolutionary consequences of decreased population size on the genetic burden of a long-lived endangered conifer with large genome size and suggest that genetic purging deserves more attention in conservation management.