The order Chaetothyriales (Pezizomycotina, Ascomycetes) harbours obligatorily melanised fungi and includes numerous etiologic agents of chromoblastomycosis, phaeohyphomycosis and other diseases of vertebrate hosts. Diseases range from mild cutaneous to fatal cerebral or disseminated infections and affect humans and cold-blooded animals globally. In addition, Chaetothyriales comprise species with aquatic, rock-inhabiting, ant-associated, and mycoparasitic life-styles, as well as species that tolerate toxic compounds, suggesting a high degree of versatile extremotolerance. To understand their biology and divergent niche occupation, we sequenced and annotated a set of 23 genomes of main the human opportunists within the Chaetothyriales as well as related environmental species. Our analyses included fungi with diverse life-styles, namely opportunistic pathogens and closely related saprobes, to identify genomic adaptations related to pathogenesis. Furthermore, ecological preferences of Chaetothyriales were analysed, in conjuncture with the order-level phylogeny based on conserved ribosomal genes. General characteristics, phylogenomic relationships, transposable elements, sex-related genes, protein family evolution, genes related to protein degradation (MEROPS), carbohydrate-active enzymes (CAZymes), melanin synthesis and secondary metabolism were investigated and compared between species. Genome assemblies varied from 25.81 Mb (Capronia coronata) to 43.03 Mb (Cladophialophora immunda). The bantiana-clade contained the highest number of predicted genes (12 817 on average) as well as larger genomes. We found a low content of mobile elements, with DNA transposons from Tc1/Mariner superfamily being the most abundant across analysed species. Additionally, we identified a reduction of carbohydrate degrading enzymes, specifically many of the Glycosyl Hydrolase (GH) class, while most of the Pectin Lyase (PL) genes were lost in etiological agents of chromoblastomycosis and phaeohyphomycosis. An expansion was found in protein degrading peptidase enzyme families S12 (serine-type D-Ala-D-Ala carboxypeptidases) and M38 (isoaspartyl dipeptidases). Based on genomic information, a wide range of abilities of melanin biosynthesis was revealed; genes related to metabolically distinct DHN, DOPA and pyomelanin pathways were identified. The MAT (MAting Type) locus and other sex-related genes were recognized in all 23 black fungi. Members of the asexual genera Fonsecaea and Cladophialophora appear to be heterothallic with a single copy of either MAT-1-1 or MAT-1-2 in each individual. All Capronia species are homothallic as both MAT1-1 and MAT1-2 genes were found in each single genome. The genomic synteny of the MAT-locus flanking genes (SLA2-APN2-COX13) is not conserved in black fungi as is commonly observed in Eurotiomycetes, indicating a unique genomic context for MAT in those species. The heterokaryon (het) genes expansion associated with the low selective pressure at the MAT-locus suggests that a parasexual cycle may play an important role in generating diversity among those fungi.

毛囊菌目（Pezizomycotina，子囊菌纲）含有必然黑化的真菌，并包括许多着色芽生菌病、褐丝菌病和脊椎动物宿主其他疾病的病原体。疾病范围从轻微的皮肤感染到致命的脑部或播散性感染，影响全球人类和冷血动物。此外，毛囊藻目还包括水生、岩石栖息、蚂蚁相关和菌寄生生活方式的物种，以及耐受有毒化合物的物种，这表明它们具有高度的多才多艺的极限运动耐受性。为了了解它们的生物学和不同的生态位占据，我们对毛囊藻目中主要人类机会主义者以及相关环境物种的 23 个基因组进行了测序和注释。我们的分析包括具有不同生活方式的真菌，即机会性病原体和密切相关的腐生菌，以识别与发病机制相关的基因组适应性。此外，结合基于保守核糖体基因的目级系统发育分析了毛藻目的生态偏好。研究并比较了物种间的一般特征、系统发育关系、转座元件、性别相关基因、蛋白质家族进化、蛋白质降解相关基因（MEROPS）、碳水化合物活性酶（CAZymes）、黑色素合成和次生代谢。基因组组装从 25.81 Mb ( Capronia coronata ) 到 43.03 Mb ( Cladophialophora immunda ) 不等。bantiana-clade 包含最多数量的预测基因（平均 12 817 个）以及更大的基因组。我们发现移动元件含量较低，来自 Tc1/Mariner 超家族的 DNA 转座子在分析的物种中最为丰富。此外，我们发现碳水化合物降解酶减少，特别是许多糖基水解酶（GH）类，而大多数果胶裂解酶（PL）基因在着色芽生菌病和暗丝菌病的病原体中丢失。在蛋白质降解肽酶家族 S12（丝氨酸型 D-Ala-D-Ala 羧肽酶）和 M38（异天冬氨酰二肽酶）中发现了扩展。基于基因组信息，揭示了黑色素生物合成的多种能力；鉴定出与代谢上不同的 DHN、DOPA 和脓黑素途径相关的基因。MAT （MA ting型）基因座和其他性别相关基因在所有23种黑真菌中均被识别。无性生殖属Fonsecaea和Cladophialophora的成员似乎是异宗合的，具有MAT-1-1或MAT-1-2的单一拷贝在每个人身上。所有Capronia物种都是同宗的，因为在每个基因组中都发现了MAT1-1和MAT1-2基因。MAT位点侧翼基因(SLA2-APN2-COX13) 的基因组同线性在黑真菌中并不像在欧洲菌纲中常见的那样保守，表明这些物种中MAT具有独特的基因组背景。与MAT位点低选择压力相关的异核 (het) 基因扩展表明，准有性循环可能在这些真菌中产生多样性方面发挥重要作用。