Grandaubert Jonathan, Dutheil Julien Y, Stukenbrock Eva H
Environmental Genomics Group Max Planck Institute for Evolutionary Biology August-Thienemann-Str. 2 24306 Plön Germany.
Christian-Albrechts University of Kiel Am Botanischen Garten 1-9 24118 Kiel Germany.
Evol Lett. 2019 May 1;3(3):299-312. doi: 10.1002/evl3.117. eCollection 2019 Jun.
Unravelling the strength, frequency, and distribution of selective variants along the genome as well as the underlying factors shaping this distribution are fundamental goals of evolutionary biology. Antagonistic host-pathogen coevolution is thought to be a major driver of genome evolution between interacting species. While rapid evolution of pathogens has been documented in several model organisms, the genetic mechanisms of their adaptation are still poorly understood and debated, particularly the role of sexual reproduction. Here, we apply a population genomic approach to infer genome-wide patterns of selection among 13 isolates of , a fungal pathogen characterized by extremely high genetic diversity, gene density, and recombination rates. We report that the genome of undergoes a high rate of adaptive substitutions, with 44% of nonsynonymous substitutions being adaptive on average. This fraction reaches 68% in so-called effector genes encoding determinants of pathogenicity, and the distribution of fitness effects differs in this class of genes as they undergo adaptive mutations with stronger positive fitness effects, but also more slightly deleterious mutations. Besides the globally high rate of adaptive substitutions, we report a negative relationship between pN/pS and the fine-scale recombination rate and a strong positive correlation between the rate of adaptive nonsynonymous substitutions (ω) and recombination rate. This result suggests a pervasive role of both background selection and Hill-Robertson interference even in a species with an exceptionally high recombination rate (60 cM/Mb on average). While transposable elements (TEs) have been suggested to contribute to adaptation by creating compartments of fast-evolving genomic regions, we do not find a significant effect of TEs on the rate of adaptive mutations. Overall our study suggests that sexual recombination is a significant driver of genome evolution, even in rapidly evolving organisms subject to recurrent mutations with large positive effects.
揭示全基因组中选择性变异的强度、频率和分布以及塑造这种分布的潜在因素是进化生物学的基本目标。宿主 - 病原体的拮抗协同进化被认为是相互作用物种间基因组进化的主要驱动力。虽然在几种模式生物中已记录了病原体的快速进化，但其适应的遗传机制仍知之甚少且存在争议，特别是有性生殖的作用。在此，我们应用群体基因组方法来推断13个 分离株全基因组的选择模式， 是一种具有极高遗传多样性、基因密度和重组率的真菌病原体。我们报告称， 的基因组经历了高频率的适应性替换，平均44%的非同义替换是适应性的。在编码致病性决定因素的所谓效应基因中，这一比例达到68%，并且这类基因的适应度效应分布有所不同，因为它们经历适应性突变时具有更强的正向适应度效应，但也有更多轻微有害的突变。除了全基因组范围的高适应性替换率，我们报告了pN/pS与精细尺度重组率之间呈负相关，以及适应性非同义替换率（ω）与重组率之间呈强正相关。这一结果表明，即使在一个平均重组率异常高（60 cM/Mb）的物种中，背景选择和希尔 - 罗伯逊干扰都具有普遍作用。虽然转座元件（TEs）被认为通过创建快速进化的基因组区域隔室来促进适应，但我们并未发现TEs对适应性突变率有显著影响。总体而言，我们的研究表明，有性重组是基因组进化的重要驱动力，即使在快速进化且受到具有大的正向效应的反复突变影响的生物体中也是如此。
