Zhu Xian-Liang, Luo Wen-Ji, Chai Sheng-Feng, Tang Jian-Min, Wei Xiao, Wee Alison K S, Kang Ming
State Key Laboratory of Plant Diversity and Specialty Crops, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, China.
University of Chinese Academy of Sciences, Beijing, China.
BMC Biol. 2025 Jun 9;23(1):161. doi: 10.1186/s12915-025-02275-y.
Vatica guangxiensis, one of the northernmost dipterocarp tree species in Asian tropical rainforests and among the most critically endangered members of the Dipterocarpaceae, faces severe genetic risks due to its extremely small population size.
We present a chromosome-scale genome assembly of V. guangxiensis, totaling 454.89 Mb, comprising 54 scaffolds (contig N50 = 38.11 Mb). To inform conservation strategies, we conducted a population genomic analysis involving 148 individuals from three natural populations of V. guangxiensis sensu lato and two of V. mangachapoi, a widely distributed tropical rainforest species in Asia. Our results clarified the population structure, interspecific differentiation, and species delimitation of V. guangxiensis sensu lato, resolving longstanding taxonomic ambiguities and supporting the reinstatement of the two Yunnan populations as V. xishuangbannaensis. Compared with V. xishuangbannaensis and V. mangachapoi, V. guangxiensis exhibits significantly lower genetic diversity, higher inbreeding, and an elevated mutation load. Additionally, we revealed a near-complete absence of gene flow with related species and documented historically low effective population sizes, underscoring its vulnerability to genome erosion. Notably, genomic comparisons between mature and regenerating individuals revealed a 26.45% decrease in genetic diversity and a 10.70% increase in mutation load in smaller trees of V. guangxiensis, reflecting accelerated genomic erosion during natural regeneration.
Our findings underscore the urgent need to monitor genomic health and implement effective conservation measures to safeguard V. guangxiensis. This study highlights the critical role of genomic data in assessing population health and informing strategies for the preservation of endangered species in marginal tropical rainforests.
广西青梅是亚洲热带雨林中最北的龙脑香科树种之一，也是龙脑香科中最濒危的成员之一，因其种群数量极少而面临严重的遗传风险。
我们展示了广西青梅的染色体水平基因组组装，总计454.89 Mb，由54个支架组成（重叠群N50 = 38.11 Mb）。为了为保护策略提供信息，我们进行了一项群体基因组分析，涉及来自广义广西青梅三个自然种群的148个个体以及亚洲广泛分布的热带雨林物种多毛坡垒的两个自然种群。我们的结果阐明了广义广西青梅的种群结构、种间分化和物种界定，解决了长期存在的分类学模糊问题，并支持将云南的两个种群恢复为西双版纳青梅。与西双版纳青梅和多毛坡垒相比，广西青梅的遗传多样性显著较低，近亲繁殖程度较高，突变负荷增加。此外，我们发现与相关物种几乎完全没有基因流，并记录了历史上较低的有效种群大小，强调了其对基因组侵蚀的脆弱性。值得注意的是，成熟个体与再生个体之间的基因组比较显示，广西青梅较小树木的遗传多样性下降了26.45%，突变负荷增加了10.70%，这反映了自然再生过程中基因组侵蚀的加速。
我们的研究结果强调了监测基因组健康状况并实施有效保护措施以保护广西青梅的迫切需求。这项研究突出了基因组数据在评估种群健康状况以及为边缘热带雨林中濒危物种的保护策略提供信息方面的关键作用。
