Hagestad Ole Christian, Hou Lingwei, Andersen Jeanette H, Hansen Espen H, Altermark Bjørn, Li Chun, Kuhnert Eric, Cox Russell J, Crous Pedro W, Spatafora Joseph W, Lail Kathleen, Amirebrahimi Mojgan, Lipzen Anna, Pangilinan Jasmyn, Andreopoulos William, Hayes Richard D, Ng Vivian, Grigoriev Igor V, Jackson Stephen A, Sutton Thomas D S, Dobson Alan D W, Rämä Teppo
Marbio, The Norwegian College of Fishery Science, Department at Faculty of Biosciences, Fisheries and Economics, UiT The Arctic University of Norway, Tromsø, Norway.
Westerdijk Fungal Biodiversity Institute, Uppsalalaan 8, 3584CT, Utrecht, Netherlands.
IMA Fungus. 2021 Aug 9;12(1):21. doi: 10.1186/s43008-021-00072-0.
Marine fungi remain poorly covered in global genome sequencing campaigns; the 1000 fungal genomes (1KFG) project attempts to shed light on the diversity, ecology and potential industrial use of overlooked and poorly resolved fungal taxa. This study characterizes the genomes of three marine fungi: Emericellopsis sp. TS7, wood-associated Amylocarpus encephaloides and algae-associated Calycina marina. These species were genome sequenced to study their genomic features, biosynthetic potential and phylogenetic placement using multilocus data. Amylocarpus encephaloides and C. marina were placed in the Helotiaceae and Pezizellaceae (Helotiales), respectively, based on a 15-gene phylogenetic analysis. These two genomes had fewer biosynthetic gene clusters (BGCs) and carbohydrate active enzymes (CAZymes) than Emericellopsis sp. TS7 isolate. Emericellopsis sp. TS7 (Hypocreales, Ascomycota) was isolated from the sponge Stelletta normani. A six-gene phylogenetic analysis placed the isolate in the marine Emericellopsis clade and morphological examination confirmed that the isolate represents a new species, which is described here as E. atlantica. Analysis of its CAZyme repertoire and a culturing experiment on three marine and one terrestrial substrates indicated that E. atlantica is a psychrotrophic generalist fungus that is able to degrade several types of marine biomass. FungiSMASH analysis revealed the presence of 35 BGCs including, eight non-ribosomal peptide synthases (NRPSs), six NRPS-like, six polyketide synthases, nine terpenes and six hybrid, mixed or other clusters. Of these BGCs, only five were homologous with characterized BGCs. The presence of unknown BGCs sets and large CAZyme repertoire set stage for further investigations of E. atlantica. The Pezizellaceae genome and the genome of the monotypic Amylocarpus genus represent the first published genomes of filamentous fungi that are restricted in their occurrence to the marine habitat and form thus a valuable resource for the community that can be used in studying ecological adaptions of fungi using comparative genomics.
海洋真菌在全球基因组测序活动中的覆盖程度仍然很低；“千种真菌基因组（1KFG）”项目试图揭示被忽视且分类尚不明确的真菌类群的多样性、生态学及潜在工业用途。本研究对三种海洋真菌的基因组进行了表征：Emericellopsis sp. TS7、与木材相关的脑形淀粉果菌（Amylocarpus encephaloides）和与藻类相关的滨海杯形菌（Calycina marina）。对这些物种进行了全基因组测序，以利用多位点数据研究它们的基因组特征、生物合成潜力和系统发育位置。基于15个基因的系统发育分析，脑形淀粉果菌和滨海杯形菌分别被归入核盘菌科（Helotiaceae）和盘菌科（Pezizellaceae，柔膜菌目）。这两个基因组的生物合成基因簇（BGC）和碳水化合物活性酶（CAZyme）比Emericellopsis sp. TS7分离株更少。Emericellopsis sp. TS7（粪壳菌纲，子囊菌门）是从诺曼氏星骨海绵（Stelletta normani）中分离出来的。一项基于六个基因的系统发育分析将该分离株置于海洋Emericellopsis分支中，形态学检查证实该分离株代表一个新物种，在此将其描述为大西洋Emericellopsis（E. atlantica）。对其CAZyme库的分析以及在三种海洋和一种陆地底物上的培养实验表明，大西洋Emericellopsis是一种嗜冷性泛养真菌，能够降解多种类型的海洋生物质。真菌生物合成基因簇分析（FungiSMASH）显示存在35个BGC，包括八个非核糖体肽合成酶（NRPS）、六个类NRPS、六个聚酮合酶、九个萜类以及六个杂合、混合或其他簇。在这些BGC中，只有五个与已表征的BGC同源。未知BGC集和大量CAZyme库的存在为进一步研究大西洋Emericellopsis奠定了基础。盘菌科基因组和单型淀粉果菌属的基因组代表了首次发表的丝状真菌基因组，它们仅出现在海洋栖息地，因此是一个宝贵的资源，可用于通过比较基因组学研究真菌的生态适应性。
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