Data from: Genome reduction uncovers a large dispensable genome and adaptive role for copy number variation in asexually propagated Solanum tuberosum

Clonally reproducing plants have the potential to bear a significantly greater mutational load than sexually reproducing species. To investigate this possibility, we examined the breadth of genome-wide structural variation in a panel of monoploid/doubled monoploid clones generated from native populations of diploid potato (Solanum tuberosum), a highly heterozygous asexually propagated plant. As rare instances of purely homozygous clones, they provided an ideal set for determining the degree of structural variation tolerated by this species, and deriving its minimal gene complement. Extensive copy number variation (CNV) was uncovered, impacting 219.8 Mb (30.2%) of the potato genome with nearly 30% of genes subject to at least partial duplication or deletion, revealing the highly heterogeneous nature of the potato genome. Dispensable genes (>7,000) were associated with limited transcription and/or a recent evolutionary history, with lower deletion frequency observed in genes conserved across angiosperms. Association of CNV with plant adaptation was highlighted by enrichment in gene clusters encoding functions for environmental stress response, with gene duplication playing a part in species-specific expansions of stress-related gene families. This study revealed unique impacts of CNV in a species with asexual reproductive habits, and how CNV may drive adaption through evolution of key stress pathways.

克隆繁殖植物相较于有性繁殖物种，理论上可承受显著更高的突变负荷。为探究这一可能性，本研究对二倍体马铃薯（Solanum tuberosum）原生种群衍生的单倍体/加倍单倍体克隆群体开展全基因组结构变异广度分析——该物种为高度杂合的无性繁殖植物。作为罕见的纯合克隆实例，该群体为解析该物种可耐受的结构变异程度、推导其最小基因组分提供了理想研究材料。研究发现大量拷贝数变异（Copy Number Variation, CNV），其覆盖马铃薯基因组219.8 Mb（占比30.2%），近30%的基因存在至少部分片段的重复或缺失，揭示了马铃薯基因组高度异质性的本质。超过7000个非必需基因与有限的转录活性及/或较新的进化历程相关，且被子植物中保守基因的缺失频率相对更低。编码环境应激响应功能的基因簇显著富集，凸显了拷贝数变异与植物适应性的关联，而基因重复在胁迫相关基因家族的物种特异性扩张中发挥了作用。本研究揭示了拷贝数变异对无性繁殖物种的独特影响，以及拷贝数变异如何通过关键应激通路的进化推动植物适应性演化。