Department of Botany and Plant Pathology, Purdue University, West Lafayette, IN.
US Department of Energy Joint Genome Institute, Walnut Creek, CA.
Mol Biol Evol. 2018 Aug 1;35(8):1840-1854. doi: 10.1093/molbev/msy072.
Ustilaginomycotina is home to a broad array of fungi including important plant pathogens collectively called smut fungi. Smuts are biotrophs that produce characteristic perennating propagules called teliospores, one of which, Ustilago maydis, is a model genetic organism. Broad exploration of smut biology has been hampered by limited phylogenetic resolution of Ustilaginiomycotina as well as an overall lack of genomic data for members of this subphylum. In this study, we sequenced eight Ustilaginomycotina genomes from previously unrepresented lineages, deciphered ordinal-level phylogenetic relationships for the subphylum, and performed comparative analyses. Unlike other Basidiomycota subphyla, all sampled Ustilaginomycotina genomes are relatively small and compact. Ancestral state reconstruction analyses indicate that teliospore formation was present at the origin of the subphylum. Divergence time estimation dates the divergence of most extant smut fungi after that of grasses (Poaceae). However, we found limited conservation of well-characterized genes related to smut pathogenesis from U. maydis, indicating dissimilar pathogenic mechanisms exist across other smut lineages. The genomes of Malasseziomycetes are highly diverged from the other sampled Ustilaginomycotina, likely due to their unique history as mammal-associated lipophilic yeasts. Despite extensive genomic data, the phylogenetic placement of this class remains ambiguous. Although the sampled Ustilaginomycotina members lack many core enzymes for plant cell wall decomposition and starch catabolism, we identified several novel carbohydrate active enzymes potentially related to pectin breakdown. Finally, ∼50% of Ustilaginomycotina species-specific genes are present in previously undersampled and rare lineages, highlighting the importance of exploring fungal diversity as a resource for novel gene discovery.
黑粉菌是一类真菌，包括许多重要的植物病原菌，统称为黑粉菌。黑粉菌是专性活体营养生物，会产生特征性的休眠孢子，即冬孢子，其中玉米黑粉菌是一种模式遗传生物体。黑粉菌生物学的广泛研究受到黑粉菌系统发育分辨率有限以及该亚门成员整体基因组数据缺乏的阻碍。在这项研究中，我们对来自以前未代表谱系的 8 个黑粉菌基因组进行了测序，解析了该亚门的目级系统发育关系，并进行了比较分析。与其他担子菌亚门不同，所有采样的黑粉菌基因组都相对较小且紧凑。祖先状态重建分析表明，冬孢子的形成存在于该亚门的起源。分歧时间估计表明，大多数现存黑粉菌的分化发生在禾本科（Poaceae）之后。然而，我们发现玉米黑粉菌中与黑粉菌发病机制相关的特征基因的保守性有限，表明其他黑粉菌谱系存在不同的致病机制。Malasseziomycetes 的基因组与其他采样的黑粉菌高度分化，可能是由于它们作为哺乳动物相关亲脂酵母的独特历史。尽管有广泛的基因组数据，但该类群的系统发育位置仍然不明确。尽管采样的黑粉菌成员缺乏许多植物细胞壁分解和淀粉代谢的核心酶，但我们鉴定了几种可能与果胶分解有关的新型碳水化合物活性酶。最后，约 50%的黑粉菌物种特异性基因存在于以前采样不足和罕见的谱系中，这突出了探索真菌多样性作为新型基因发现资源的重要性。
