Teixeira M M, Moreno L F, Stielow B J, Muszewska A, Hainaut M, Gonzaga L, Abouelleil A, Patané J S L, Priest M, Souza R, Young S, Ferreira K S, Zeng Q, da Cunha M M L, Gladki A, Barker B, Vicente V A, de Souza E M, Almeida S, Henrissat B, Vasconcelos A T R, Deng S, Voglmayr H, Moussa T A A, Gorbushina A, Felipe M S S, Cuomo C A, de Hoog G Sybren
Division of Pathogen Genomics, Translational Genomics Research Institute (TGen), Flagstaff, AZ, USA; Department of Cell Biology, University of Brasília, Brasilia, Brazil.
Westerdijk Fungal Biodiversity Institute, Utrecht, The Netherlands; Department of Basic Pathology, Federal University of Paraná State, Curitiba, PR, Brazi1; Institute of Biodiversity and Ecosystem Dynamics, University of Amsterdam, Amsterdam, The Netherlands.
Stud Mycol. 2017 Mar;86:1-28. doi: 10.1016/j.simyco.2017.01.001. Epub 2017 Jan 27.
The order (, ) 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, 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 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 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 () to 43.03 Mb (). 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 (ting ype) locus and other sex-related genes were recognized in all 23 black fungi. Members of the asexual genera and appear to be heterothallic with a single copy of either or in each individual. All species are homothallic as both and genes were found in each single genome. The genomic synteny of the -locus flanking genes (SLA2-APN2-COX13) is not conserved in black fungi as is commonly observed in , indicating a unique genomic context for in those species. The heterokaryon (het) genes expansion associated with the low selective pressure at the -locus suggests that a parasexual cycle may play an important role in generating diversity among those fungi.
该目（ ， ）必然包含黑色素化真菌，包括许多引起着色芽生菌病、暗色丝孢霉病及其他脊椎动物宿主疾病的病原体。这些疾病范围从轻度皮肤感染到致命的脑部感染或播散性感染，全球范围内影响人类和冷血动物。此外， 包含具有水生、栖息于岩石、与蚂蚁相关以及真菌寄生生活方式的物种，还有耐受有毒化合物的物种，这表明它们具有高度的多功能极端耐受性。为了解它们的生物学特性和不同的生态位占据情况，我们对该目中主要人类机会致病菌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，即机会性病原菌和密切相关的腐生菌，以确定与致病机制相关的基因组适应性变化。此外，结合基于保守核糖体基因的目级系统发育，分析了 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、与蛋白质降解相关的基因（MEROPS）、碳水化合物活性酶（CAZymes）、黑色素合成和次级代谢。基因组组装大小从25.81 Mb（ ）到43.03 Mb（ ）不等。班替枝（bantiana-clade）包含的预测基因数量最多（平均12 817个），基因组也更大。我们发现移动元件含量较低，在分析的物种中，来自Tc1/Mariner超家族的DNA转座子最为丰富。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，而在着色芽生菌病和暗色丝孢霉病的病原体中，大多数果胶裂解酶（PL）基因丢失。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）中发现了基因扩增。基于基因组信息，揭示了黑色素生物合成的广泛能力；鉴定出与代谢不同的二羟基萘（DHN）、多巴和脓黑素途径相关的基因。在所有23种黑色真菌中都识别出了（ting ype）位点和其他性别相关基因。无性属 和 的成员似乎是异宗配合的，每个个体中 或 只有一个拷贝。所有 物种都是同宗配合的，因为在每个单倍体基因组中都发现了 和 基因。与 位点低选择压力相关的异核体（het）基因扩增表明，准性生殖周期可能在这些真菌的多样性产生中起重要作用。
