Wei Kai, Stam Remco, Tellier Aurélien, Silva-Arias Gustavo A
Xinjiang Key Laboratory of Biological Resources and Genetic Engineering, College of Life Science and Technology, Xinjiang University, Urumqi 830049, China.
Population Genetics, Department of Life Science Systems, School of Life Sciences, Technical University of Munich, Freising 85354, Germany.
Mol Biol Evol. 2025 Jul 30;42(8). doi: 10.1093/molbev/msaf191.
Copy Number Variation (CNV) is a prevalent type of variation affecting large genomic regions which contributes to both genetic diversity and ecological adaptation in plants. The target genes involved in adaptation through CNV in tomato and its wild relatives remain unexplored at the population level. Therefore, we characterized the CNV landscape of Solanum chilense, a wild tomato species adapted to dry habitats, using whole-genome short-read data of 35 individuals from 7 populations. We identified 212,207 CNVs, including 160,926 deletions and 51,281 duplications. We found a higher number of CNVs in diverging populations occupying stressful habitats. CNVs and single-nucleotide polymorphism analyses concordantly revealed the known species' population structure, underscoring the impact of historical demographic and recent colonization events shaping genome-wide CNVs. Furthermore, we identified 3,539 candidate genes with highly divergent CNV profiles across populations. Interestingly, these genes are functionally associated with response to abiotic stress and linked to multiple pathways of flowering time regulation. Gene CNVs in S. chilense exhibit 2 evolutionary trends: gene loss in ancestral lineages distributed in central and southern coast populations and gene gain in the most recent diverged lineage from the southern highland region. Environmental association of the CNVs ultimately linked the dynamics of gene copy number to 6 climatic variables. It suggests that natural selection has likely shaped CNV patterns in stress-response genes, promoting the colonization of contrasting habitats. Our findings provide insights into the role of CNV underlying adaptation during recent range expansion.
拷贝数变异（CNV）是一种常见的变异类型，会影响大片段基因组区域，对植物的遗传多样性和生态适应性均有贡献。番茄及其野生近缘种中通过拷贝数变异参与适应性的目标基因在种群水平上仍未得到探索。因此，我们利用来自7个种群的35个个体的全基因组短读数据，对适应干旱生境的野生番茄物种智利番茄的拷贝数变异图谱进行了表征。我们鉴定出212,207个拷贝数变异，包括160,926个缺失和51,281个重复。我们发现在占据压力生境的分化种群中拷贝数变异数量更多。拷贝数变异和单核苷酸多态性分析一致地揭示了已知的物种种群结构，突出了历史种群统计学和近期殖民事件对全基因组拷贝数变异形成的影响。此外，我们鉴定出3539个在种群间具有高度差异拷贝数变异图谱的候选基因。有趣的是，这些基因在功能上与非生物胁迫响应相关，并与开花时间调控的多个途径有关。智利番茄中的基因拷贝数变异呈现出两种进化趋势：分布在中部和南部海岸种群的祖先谱系中基因丢失，以及来自南部高地地区最近分化谱系中的基因获得。拷贝数变异与环境的关联最终将基因拷贝数动态与6个气候变量联系起来。这表明自然选择可能塑造了胁迫响应基因中的拷贝数变异模式，促进了对不同生境的殖民化。我们的研究结果为近期范围扩张过程中拷贝数变异在适应过程中的作用提供了见解。
