A small subset of NLR genes drives local adaptation to pathogens in wild tomato
A small subset of NLR genes drives local adaptation to pathogens in wild tomato
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DOI：
10.1101/210559
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发表时间：
2017-10
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影响因子：
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通讯作者：
R. Stam;Gustavo A. Silva-Arias;T. Nosenko;Daniela Scheikl;Anja C. Hörger;W. Stephan;G. Haberer;A. Tellier
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文献类型：
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作者：
R. Stam;Gustavo A. Silva-Arias;T. Nosenko;Daniela Scheikl;Anja C. Hörger;W. Stephan;G. Haberer;A. Tellier
在植物中，包括NLR基因家族在内的防御相关基因被认为处于不断进化的压力下以适应病原体。目前仍不清楚有多少NLR有助于适应，以及是否涉及的基因座在不同栖息地的物种内有所不同。我们使用了一个三管齐下的方法来揭示和量化的选择签名超过90 NLR基因从14个种群的茄，野生番茄物种特有的秘鲁和智利发现在不同的栖息地。首先，我们构建了一个S.智利人。其次，对三个地理位置遥远的个体进行全基因组重新测序，使我们能够推断该物种过去栖息地殖民的人口统计历史。最后，使用有针对性的重测序，我们表明，一个小的NLR子集，7%，显示积极或平衡选择的迹象。我们证明，13个NLR改变方向的选择在新的栖息地的殖民化，并形成一个马赛克模式的适应病原体。我们估计NLR上选择的转换时间（出生率和死亡率）为18，000年。最后，我们的工作确定了新的NLR在栖息地之间的强选择压力，从而为R-基因识别提供了新的机会。
In plants, defence-associated genes including the NLR gene family are thought to be under constant evolutionary pressure to adapt to pathogens. It is still unknown how many NLRs contribute to adaptation, and if the involved loci vary within a species across habitats. We used a three-pronged approach to reveal and quantify selection signatures at over 90 NLR genes from 14 populations of Solanum chilense, a wild tomato species endemic to Peru and Chile found in diverse habitats. First, we generated a de novo genome of S. chilense. Second, whole genome resequencing of three geographically distant individuals allows us to infer the species’ past demographic history of habitat colonisation. Finally, using targeted resequencing we show that a small subset of NLRs, 7%, show signs of positive or balancing selection. We demonstrate that 13 NLRs change direction of selection during the colonisation of new habitats and form a mosaic pattern of adaptation to pathogens. We estimate that the turn over time of selection (birth and death rate) on NLRs is 18,000 years. Finally, our work identifies new NLRs under strong selective pressure between habitats, thus providing novel opportunities for R-gene identification.