Derbyshire Mark C
Centre for Crop and Disease Management, School of Molecular and Life Sciences, Curtin University, Perth, WA, Australia.
Front Microbiol. 2020 Apr 9;11:644. doi: 10.3389/fmicb.2020.00644. eCollection 2020.
The genomes of plant pathogenic fungi and oomycetes are often exposed to strong positive selection pressure. During speciation, shifts in host range and preference can lead to major adaptive changes. Furthermore, evolution of total host resistance to most isolates can force rapid evolutionary changes in host-specific pathogens. Crop pathogens are subjected to particularly intense selective pressures from monocultures and fungicides. Detection of the footprints of positive selection in plant pathogen genomes is a worthwhile endeavor as it aids understanding of the fundamental biology of these important organisms. There are two main classes of test for detection of positively selected alleles. Tests based on the ratio of non-synonymous to synonymous substitutions per site detect the footprints of multiple fixation events between divergent lineages. Thus, they are well-suited to the study of ancient adaptation events spanning speciations. On the other hand, tests that scan genomes for local fluctuations in allelic diversity within populations are suitable for detection of recent positive selection in populations. In this review, I briefly describe some of the more widely used tests of positive selection and the theory underlying them. I then discuss various examples of their application to plant pathogen genomes, emphasizing the types of genes that are associated with signatures of positive selection. I conclude with a discussion of the practicality of such tests for identification of pathogen genes of interest and the important features of pathogen ecology that must be taken into account for accurate interpretation.
植物病原真菌和卵菌的基因组常常面临强大的正选择压力。在物种形成过程中，宿主范围和偏好的转变可能导致重大的适应性变化。此外，对大多数分离株的完全宿主抗性的进化会迫使宿主特异性病原体发生快速的进化变化。作物病原体受到来自单一栽培和杀真菌剂的特别强烈的选择压力。检测植物病原体基因组中的正选择印记是一项有价值的工作，因为它有助于理解这些重要生物体的基础生物学。检测正选择等位基因主要有两类测试。基于每个位点非同义替换与同义替换比率的测试可检测不同谱系之间多个固定事件的印记。因此，它们非常适合研究跨越物种形成的古代适应事件。另一方面，扫描基因组以寻找种群内等位基因多样性局部波动的测试适用于检测种群中近期的正选择。在这篇综述中，我简要描述一些更广泛使用的正选择测试及其背后的理论。然后我讨论它们应用于植物病原体基因组的各种例子，重点强调与正选择特征相关的基因类型。最后，我讨论此类测试用于鉴定感兴趣的病原体基因的实用性以及准确解释时必须考虑的病原体生态学的重要特征。
