Circumfusicillium cavernae gen. et sp. nov. (Bionectriaceae, Hypocreales) isolated from a hypogean Roman cryptoporticus

Phylogenetic alignments and trees<br>Article abstract: During the ongoing studies designed to examine the fungal diversity present within the abandoned and flooded Escádia Grande gold mine (Góis, Portugal), we repeatedly isolated several specimens belonging to a <i>Penicillium</i> species. Molecular phylogenetic analysis, coupled with morphological observations, positioned this fungus within subgen. <i>Penicillium</i> sect. <i>Paradoxa</i>, series <i>Atramentosa</i>, pinpointing its identity as <i>Penicillium mexicanum</i> (the first record for mining soils and the country). Given the limited research conducted on <i>Penicillia</i> isolated from similar environments, the species genome was sequenced utilizing the Oxford Nanopore^® MinION^™ methodology and studied through bioinformatic analysis. The obtained genome has a size of 29.62 Mb, containing a 47.72% GC content, 10,156 genes, with 44 rRNAs and 178 tRNAs/tmRNAs, providing the first genomic resource for this microorganism. Bioinformatic analysis allowed us to identify multiple genomic traits that can contribute towards this species survival in these extreme environments, including the presence of high levels of major facilitator transporters (MFS), Zn (2)-C6 fungal-type DNA-binding domains, P-loop containing nucleoside triphosphate hydrolases, specific fungal transcription factors and sugar transporters. Furthermore, putative advantageous metabolic traits, such as methylotrophy, assimilatory nitrate and sulfate reduction abilities, were also detected. In addition, the results also highlighted a strong genomic and metabolic organization and investment towards arsenic detoxification (transport and oxidation). Lastly, thirty-two putative biosynthetic gene clusters were predicted, including some with high similarity values to monascorubrin, nidulanin A, histidyltryptophanyldiketopiperazine/dehydrohistidyltryptophanyldiketopiperazine/roquefortine D/roquefortine C/glandicoline A/glandicoline B/meleagrine, YWA1 and choline. Overall, this study expands the current <i>Penicillia</i> knowledge from mining environments while also enhancing our understanding regarding fungal arsenic resistance.

系统发育比对与系统发育树
文章摘要：本研究针对葡萄牙戈伊斯地区废弃积水的埃斯卡迪亚格兰德（Escádia Grande）金矿中的真菌多样性展开调查，期间多次分离得到多份隶属于青霉属（*Penicillium*）的菌株标本。结合分子系统发育分析与形态学观察，该真菌被归类于青霉亚属（subgen. *Penicillium*）的奇异青霉组（sect. *Paradoxa*）、暗紫青霉系（series *Atramentosa*），经鉴定为墨西哥青霉（*Penicillium mexicanum*）——这是该物种在采矿土壤及葡萄牙境内的首次记录。鉴于目前针对类似环境中分离的青霉属真菌的研究较为匮乏，本研究采用牛津纳米孔（Oxford Nanopore®）MinION™测序技术对该物种的基因组进行测序，并通过生物信息学手段开展分析。所获得的基因组大小为29.62 Mb，GC含量为47.72%，共编码10156个基因，包含44个核糖体RNA（rRNA）基因及178个转运RNA/转运信使RNA（tRNAs/tmRNAs）基因，为该微生物提供了首个基因组资源。生物信息学分析揭示了多个可助力该物种在极端环境中存活的基因组特征，包括高丰度的主要促进因子超家族（MFS）转运蛋白、Zn(2)-C6真菌型DNA结合结构域、含P-loop的核苷三磷酸水解酶、特异性真菌转录因子以及糖转运蛋白。此外，本研究还检测到若干潜在的有益代谢特征，例如甲基营养型代谢、同化型硝酸盐还原与硫酸盐还原能力。此外，研究结果还显示该物种在砷解毒（转运与氧化）相关的基因组与代谢通路方面存在显著的组织化特征与资源投入。最后，本研究共预测得到32个潜在的生物合成基因簇，其中部分基因簇与红曲黄素（monascorubrin）、尼杜兰菌素A（nidulanin A）、组氨酰色氨酰二酮哌嗪/脱氢组氨酰色氨酰二酮哌嗪/洛克非特碱D/洛克非特碱C/腺柯林A/腺柯林B/美雀灵（histidyltryptophanyldiketopiperazine/dehydrohistidyltryptophanyldiketopiperazine/roquefortine D/roquefortine C/glandicoline A/glandicoline B/meleagrine）、YWA1以及胆碱（choline）具有较高的序列相似性。综上，本研究拓展了学界对采矿环境中青霉属真菌的认知，同时加深了我们对真菌砷抗性机制的理解。