Tests based on the dN/dS statistic are used to identify positive selection of nonsynonymous polymorphisms. Using these tests on alignments of all orthologs from related species can provide insights into which gene categories have been most frequently positively selected. However, longer alignments have more power to detect positive selection, creating a detection bias that could create misleading results from functional enrichment tests. Most studies of positive selection in plant pathogens focus on genes with specific virulence functions, with little emphasis on broader molecular processes. Furthermore, no studies in plant pathogens have accounted for detection bias due to alignment length when performing functional enrichment tests. To address these research gaps, we analyze 12 genomes of the phytopathogenic fungal genus Botrytis, including two sequenced in this study. To establish a temporal context, we estimated fossil-calibrated divergence times for the genus. We find that Botrytis likely originated 16–18 Ma in the Miocene and underwent continuous radiation ending in the Pliocene. An untargeted scan of Botrytis single-copy orthologs for positive selection with three different statistical tests uncovered evidence for positive selection among proteases, signaling proteins, CAZymes, and secreted proteins. There was also a strong overrepresentation of transcription factors among positively selected genes. This overrepresentation was still apparent after two complementary controls for detection bias due to sequence length. Positively selected sites were depleted within DNA-binding domains, suggesting changes in transcriptional responses to internal and external cues or protein–protein interactions have undergone positive selection more frequently than changes in promoter fidelity.

中文翻译：

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转录因子的正选择是起源于中新世的植物病原属进化的一个显着特征

基于 dN/dS 统计量的测试用于识别非同义多态性的阳性选择。对来自相关物种的所有直系同源物的比对使用这些测试可以提供关于哪些基因类别最常被积极选择的见解。然而，较长的比对更有能力检测阳性选择，从而产生检测偏差，可能会从功能富集测试中产生误导性结果。大多数关于植物病原体正选择的研究都集中在具有特定毒力功能的基因上，很少强调更广泛的分子过程。此外，在进行功能富集测试时，没有关于植物病原体的研究考虑到由于对齐长度而导致的检测偏差。为了解决这些研究空白，我们分析了植物病原真菌 Botrytis 的 12 个基因组，包括本研究中测序的两个。为了建立时间背景，我们估计了该属的化石校准分歧时间。我们发现灰霉病可能起源于中新世的 16-18 Ma，并在上新世经历了持续的辐射。用三种不同的统计测试对葡萄孢属单拷贝直系同源物进行非靶向扫描以进行阳性选择，揭示了在蛋白酶、信号蛋白、CAZymes 和分泌蛋白之间进行阳性选择的证据。在阳性选择的基因中，转录因子也有很强的过度表现。由于序列长度导致的检测偏差在两个互补控制后，这种过度表现仍然很明显。阳性选择的位点在 DNA 结合域内被耗尽，