Genes for ash tree resistance to an insect pest identified via comparative genomics
Genes for ash tree resistance to an insect pest identified via comparative genomics
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DOI：
10.1101/772913
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发表时间：
2019-09
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影响因子：
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通讯作者：
L. J. Kelly;W. Plumb;D. Carey;M. Mason;E. Cooper;William Crowther;A. Whittemore;S. Rossiter
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文献类型：
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作者：
L. J. Kelly;W. Plumb;D. Carey;M. Mason;E. Cooper;William Crowther;A. Whittemore;S. Rossiter
一个物种内功能性状候选基因的全基因组发现通常需要对表型个体的大量样本进行测序1，或通过多代进行连锁分析2。当一个性状在一个属内系统发育独立的谱系中反复出现时，更有效的方法可能是通过检测具有该性状的物种共有的氨基酸残基来识别基因3,4。在这里，通过采用这种方法，我们在白蜡树属（灰树）中确定了对翠绿灰螟甲虫（EAB; Agrilus planipennis）具有抗性的候选位点，这种害虫物种在其原产的东亚范围内对其他健康的白蜡树无害，但在北美具有高度破坏性，并对欧洲的白蜡树构成威胁。研究人员对白蜡树的24个二倍体种和亚种进行全基因组测序，并通过卵生物测定对26个类群的EAB抗性进行了估计，发现53个基因含有的氨基酸变异在两个或多个独立的白蜡树谱系与EAB抗性物种之间共享，这些变异不太可能是由于偶然或未被发现的同源性。其中，7个基因被认为与苯丙素生物合成途径有关，17个基因可能与食草动物识别、防御信号传导或程序性细胞死亡有关。我们还发现，在我们的53个候选基因中，可能的功能丧失突变在易感物种中比在耐药物种中更常见。在代表不同欧洲种群的白蜡树中，EAB相关氨基酸变异的多态性模式表明，选择可能能够增强它们对EAB的抗性。
Genome-wide discovery of candidate genes for functional traits within a species typically involves the sequencing of large samples of phenotyped individuals1, or linkage analysis through multiple generations2. When a trait occurs repeatedly among phylogenetically independent lineages within a genus, a more efficient approach may be to identify genes via detection of amino acid residues shared by species possessing that trait3,4. Here, by taking this approach, we identify candidate loci in the genus Fraxinus (ash trees) for resistance to the emerald ash borer beetle (EAB; Agrilus planipennis), a pest species that appears innocuous to otherwise healthy ash in its native East Asian range5 but is highly destructive in North America6 and poses a threat to ash trees in Europe7. Assembling whole genome sequences for 24 diploid species and subspecies of ash, and estimating resistance to EAB for 26 taxa from egg bioassays, we find 53 genes containing amino acid variants shared between two or more independent Fraxinus lineages with EAB-resistant species, that are unlikely to be due to chance or undetected paralogy. Of these, seven genes have putative roles relating to the phenylpropanoid biosynthesis pathway and 17 are potentially connected to herbivore recognition, defence signalling or programmed cell death. We also find that possible loss-of-function mutations among our 53 candidate genes are more frequent in susceptible species, than in resistant ones. Patterns of polymorphism for the EAB-associated amino acid variants in ash trees representing different European populations suggest that selection may be able to enhance their resistance to EAB.