Genome Reduction Uncovers a Large Dispensable Genome and Adaptive Role for Copy Number Variation in Asexually Propagated Solanum tuberosum
Genome Reduction Uncovers a Large Dispensable Genome and Adaptive Role for Copy Number Variation in Asexually Propagated Solanum tuberosum
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DOI：
10.1105/tpc.15.00538
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发表时间：
2016-02-01
期刊：
影响因子：
11.6
通讯作者：
Buell, C. Robin
中科院分区：
文献类型：
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作者：
Hardigan, Michael A.;Crisovan, Emily;Buell, C. Robin
无性繁殖植物比有性繁殖的物种有可能承受更大的突变负荷。为了研究这种可能性，我们研究了从二倍体马铃薯（Solanum tuberosum）（一种高度杂合的无性繁殖植物）的本地种群产生的一组单倍体/加倍单倍体克隆的全基因组结构变异的宽度。作为纯合克隆的罕见实例，它们为确定该物种所耐受的结构变异程度和推导其最小基因互补提供了理想的集合。广泛的拷贝数变异（CNV）被发现，影响219.8 Mb（30.2%）的马铃薯基因组，近30%的基因至少部分重复或缺失，揭示了马铃薯基因组的高度异质性。可分配基因（>7000个）与有限的转录和/或最近的进化史有关，在被子植物中保守的基因中观察到较低的缺失频率。CNV与植物适应的关联突出了编码环境胁迫响应功能的基因簇的富集，其中基因重复在胁迫相关基因家族的物种特异性扩增中发挥作用。这项研究揭示了CNV在具有无性生殖习惯的物种中的独特影响，以及CNV如何通过关键应激途径的进化来驱动适应。
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 (>7000) 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.