Muggia Lucia, Ametrano Claudio G, Sterflinger Katja, Tesei Donatella
Department of Life Sciences, University of Trieste, 34127 Trieste, Italy.
Grainger Bioinformatics Center, Department of Science and Education, Chicago, IL 60605, USA.
Life (Basel). 2020 Dec 17;10(12):356. doi: 10.3390/life10120356.
Fungi are among the most successful eukaryotes on Earth: they have evolved strategies to survive in the most diverse environments and stressful conditions and have been selected and exploited for multiple aims by humans. The characteristic features intrinsic of Fungi have required evolutionary changes and adaptations at deep molecular levels. Omics approaches, nowadays including genomics, metagenomics, phylogenomics, transcriptomics, metabolomics, and proteomics have enormously advanced the way to understand fungal diversity at diverse taxonomic levels, under changeable conditions and in still under-investigated environments. These approaches can be applied both on environmental communities and on individual organisms, either in nature or in axenic culture and have led the traditional morphology-based fungal systematic to increasingly implement molecular-based approaches. The advent of next-generation sequencing technologies was key to boost advances in fungal genomics and proteomics research. Much effort has also been directed towards the development of methodologies for optimal genomic DNA and protein extraction and separation. To date, the amount of proteomics investigations in Ascomycetes exceeds those carried out in any other fungal group. This is primarily due to the preponderance of their involvement in plant and animal diseases and multiple industrial applications, and therefore the need to understand the biological basis of the infectious process to develop mechanisms for biologic control, as well as to detect key proteins with roles in stress survival. Here we chose to present an overview as much comprehensive as possible of the major advances, mainly of the past decade, in the fields of genomics (including phylogenomics) and proteomics of Ascomycota, focusing particularly on those reporting on opportunistic pathogenic, extremophilic, polyextremotolerant and lichenized fungi. We also present a review of the mostly used genome sequencing technologies and methods for DNA sequence and protein analyses applied so far for fungi.
它们已经进化出在最多样化的环境和压力条件下生存的策略，并被人类选择和利用以实现多种目的。真菌固有的特征需要在深层次分子水平上进行进化变化和适应。如今，组学方法包括基因组学、宏基因组学、系统发育基因组学、转录组学、代谢组学和蛋白质组学，极大地推进了我们在不同分类水平、多变条件下以及仍未充分研究的环境中理解真菌多样性的方式。这些方法既可以应用于环境群落，也可以应用于单个生物体，无论是在自然环境中还是在无菌培养中，并且已促使传统的基于形态学的真菌分类学越来越多地采用基于分子的方法。下一代测序技术的出现是推动真菌基因组学和蛋白质组学研究进展的关键。人们还投入了大量精力来开发用于优化基因组DNA和蛋白质提取与分离的方法。迄今为止，子囊菌门中的蛋白质组学研究数量超过了在任何其他真菌类群中进行的研究。这主要是由于它们在动植物疾病和多种工业应用中占主导地位，因此需要了解感染过程的生物学基础以开发生物控制机制，以及检测在应激生存中起作用的关键蛋白质。在这里，我们选择尽可能全面地概述子囊菌门在基因组学（包括系统发育基因组学）和蛋白质组学领域的主要进展，主要是过去十年的进展，特别关注那些报道机会性致病真菌、嗜极端真菌、多极端耐受真菌和地衣化真菌的研究。我们还对迄今为止用于真菌的最常用基因组测序技术以及DNA序列和蛋白质分析方法进行了综述。
