Gómez-Pérez Daniel, Kemen Eric
Center for Plant Molecular Biology (ZMBP), University of Tübingen, 72074 Tübingen, Germany.
Pathogens. 2021 Jun 25;10(7):807. doi: 10.3390/pathogens10070807.
As evidenced in parasitism, host and niche shifts are a source of genomic and phenotypic diversification. Exemplary is a reduction in the core metabolism as parasites adapt to a particular host, while the accessory genome often maintains a high degree of diversification. However, selective pressures acting on the genome of organisms that have undergone recent lifestyle or host changes have not been fully investigated. Here, we developed a comparative genomics approach to study underlying adaptive trends in oomycetes, a eukaryotic phylum with a wide and diverse range of economically important plant and animal parasitic lifestyles. Our analysis reveals converging evolution on biological processes for oomycetes that have similar lifestyles. Moreover, we find that certain functions, in particular carbohydrate metabolism, transport, and signaling, are important for host and environmental adaptation in oomycetes. Given the high correlation between lifestyle and genome properties in our oomycete dataset, together with the known convergent evolution of fungal and oomycete genomes, we developed a model that predicts plant pathogenic lifestyles with high accuracy based on functional annotations. These insights into how selective pressures correlate with lifestyle may be crucial to better understand host/lifestyle shifts and their impact on the genome.
正如在寄生现象中所证明的那样，宿主和生态位的转变是基因组和表型多样化的一个来源。典型的例子是，随着寄生虫适应特定宿主，其核心代谢会减少，而附属基因组通常保持高度的多样性。然而，作用于近期经历了生活方式或宿主变化的生物体基因组的选择压力尚未得到充分研究。在这里，我们开发了一种比较基因组学方法，以研究卵菌纲中的潜在适应性趋势，卵菌纲是一个真核生物门，具有广泛多样的经济上重要的植物和动物寄生生活方式。我们的分析揭示了具有相似生活方式的卵菌纲在生物过程上的趋同进化。此外，我们发现某些功能，特别是碳水化合物代谢、运输和信号传导，对卵菌纲适应宿主和环境很重要。鉴于我们卵菌纲数据集中生活方式与基因组特性之间的高度相关性，以及真菌和卵菌纲基因组已知的趋同进化，我们开发了一个基于功能注释能高精度预测植物致病生活方式的模型。这些关于选择压力如何与生活方式相关的见解，对于更好地理解宿主/生活方式转变及其对基因组的影响可能至关重要。
