Dothideomycetes is the largest class of kingdom Fungi and comprises an incredible diversity of lifestyles, many of which have evolved multiple times. Plant pathogens represent a major ecological niche of the class Dothideomycetes and they are known to infect most major food crops and feedstocks for biomass and biofuel production. Studying the ecology and evolution of Dothideomycetes has significant implications for our fundamental understanding of fungal evolution, their adaptation to stress and host specificity, and practical implications with regard to the effects of climate change and on the food, feed, and livestock elements of the agro-economy. In this study, we present the first large-scale, whole-genome comparison of 101 Dothideomycetes introducing 55 newly sequenced species. The availability of whole-genome data produced a high-confidence phylogeny leading to reclassification of 25 organisms, provided a clearer picture of the relationships among the various families, and indicated that pathogenicity evolved multiple times within this class. We also identified gene family expansions and contractions across the Dothideomycetes phylogeny linked to ecological niches providing insights into genome evolution and adaptation across this group. Using machine-learning methods we classified fungi into lifestyle classes with >95 % accuracy and identified a small number of gene families that positively correlated with these distinctions. This can become a valuable tool for genome-based prediction of species lifestyle, especially for rarely seen and poorly studied species.

Dothideomycetes是真菌界中最大的一类，包括令人难以置信的多样化生活方式，其中许多已经进化了多次。植物病原体代表了Dothideomycetes 类的主要生态位，已知它们会感染大多数主要的粮食作物和用于生物质和生物燃料生产的原料。研究Dothideomycetes的生态学和进化对于我们对真菌进化的基本理解、它们对压力和宿主特异性的适应以及对气候变化的影响以及对农业的食物、饲料和牲畜元素的实际影响具有重要意义-经济。在这项研究中，我们首次对 101 种Dothideomycetes进行大规模全基因组比较引入 55 个新测序的物种。全基因组数据的可用性产生了高可信度的系统发育，导致对 25 种生物进行重新分类，提供了各个科之间关系的更清晰图景，并表明致病性在该类别中进化了多次。我们还确定了Dothideomycetes 的基因家族扩张和收缩与生态位相关的系统发育为该群体的基因组进化和适应提供了见解。使用机器学习方法，我们以 >95% 的准确度将真菌分类为生活方式类别，并确定了少数与这些区别正相关的基因家族。这可以成为基于基因组预测物种生活方式的宝贵工具，特别是对于很少见和研究不足的物种。