Dark septate endophytes (DSE) are a form-group of root endophytic fungi with elusive functions. Here, the genomes of two common DSE of semiarid areas, Cadophora sp. and Periconia macrospinosa were sequenced and analyzed with another 32 ascomycetes of different lifestyles. Cadophora sp. (Helotiales) and P. macrospinosa (Pleosporales) have genomes of 70.46 Mb and 54.99 Mb with 22,766 and 18,750 gene models, respectively. The majority of DSE-specific protein clusters lack functional annotation with no similarity to characterized proteins, implying that they have evolved unique genetic innovations. Both DSE possess an expanded number of carbohydrate active enzymes (CAZymes), including plant cell wall degrading enzymes (PCWDEs). Those were similar in three other DSE, and contributed a signal for the separation of root endophytes in principal component analyses of CAZymes, indicating shared genomic traits of DSE fungi. Number of secreted proteases and lipases, aquaporins, and genes linked to melanin synthesis were also relatively high in our fungi. In spite of certain similarities between our two DSE, we observed low levels of convergence in their gene family evolution. This suggests that, despite originating from the same habitat, these two fungi evolved along different evolutionary trajectories and display considerable functional differences within the endophytic lifestyle.

中文翻译：

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比较基因组学提供了对生活方式的深入了解，并揭示了深色有隔内生真菌的功能异质性。


深色有隔内生真菌（DSE）是一类具有难以捉摸功能的根部内生真菌。在这里，半干旱地区两种常见的 DSE（Cadophora sp.）的基因组。对另外 32 种不同生活方式的子囊菌进行了测序和分析。 Cadophora sp。 Helotiales 和 Pleosporales 的基因组分别为 70.46 Mb 和 54.99 Mb，分别有 22,766 和 18,750 个基因模型。大多数 DSE 特异性蛋白质簇缺乏功能注释，与特征蛋白质没有相似性，这意味着它们已经进化出独特的遗传创新。两种 DSE 都拥有数量更多的碳水化合物活性酶 (CAZymes)，包括植物细胞壁降解酶 (PCWDE)。这些在其他三个 DSE 中是相似的，并且为 CAZymes 主成分分析中根内生菌的分离提供了信号，表明 DSE 真菌具有共同的基因组特征。在我们的真菌中，分泌的蛋白酶和脂肪酶、水通道蛋白以及与黑色素合成相关的基因的数量也相对较高。尽管我们的两个 DSE 之间存在某些相似之处，但我们观察到它们的基因家族进化的趋同程度较低。这表明，尽管起源于相同的栖息地，但这两种真菌沿着不同的进化轨迹进化，并且在内生生活方式中表现出相当大的功能差异。