Faculty of Medicine, University of Brasília, Brasília 70910-900, Brazil.
The Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, AZ 86011, USA.
G3 (Bethesda). 2022 Apr 4;12(4). doi: 10.1093/g3journal/jkac031.
Coccidioidomycosis is a common fungal disease that is endemic to arid and semi-arid regions of both American continents. Coccidioides immitis and Coccidioides posadasii are the etiological agents of the disease, also known as Valley Fever. For several decades, the C. posadasii strain Silveira has been used widely in vaccine studies, is the source strain for production of diagnostic antigens, and is a widely used experimental strain for functional studies. In 2009, the genome was sequenced using Sanger sequencing technology, and a draft assembly and annotation were made available. In this study, the genome of the Silveira strain was sequenced using single molecule real-time sequencing PacBio technology, assembled into chromosomal-level contigs, genotyped, and the genome was reannotated using sophisticated and curated in silico tools. This high-quality genome sequencing effort has improved our understanding of chromosomal structure, gene set annotation, and lays the groundwork for identification of structural variants (e.g. transversions, translocations, and copy number variants), assessment of gene gain and loss, and comparison of transposable elements in future phylogenetic and population genomics studies.
球孢子菌病是一种常见的真菌病，流行于美洲大陆的干旱和半干旱地区。粗球孢子菌和波氏球孢子菌是该病的病原体，也称为山谷热。几十年来，Silveira 型 C. posadasii 菌株已广泛用于疫苗研究，是生产诊断抗原的来源菌株，也是功能研究的常用实验菌株。2009 年，使用 Sanger 测序技术对其基因组进行测序，并提供了一个草案组装和注释。在这项研究中，使用单分子实时测序 PacBio 技术对 Silveira 株的基因组进行测序，组装成染色体水平的连续序列，进行基因分型，并使用复杂的和经过精心整理的计算工具重新注释基因组。这项高质量的基因组测序工作提高了我们对染色体结构、基因集注释的理解，并为鉴定结构变异（例如转换、易位和拷贝数变异）、评估基因增益和缺失以及比较转座元件奠定了基础，未来的系统发育和群体基因组学研究。
