A chromosomal-level reference genome of the widely utilized Coccidioides posadasii laboratory strain “Silveira”

Abstract

Coccidioidomycosis is a common fungal disease that is endemic to arid and semi-arid regions of both American continents. Coccidioides immitis and C. 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 was made available. In the current study, the genome of the Silveira strain was sequenced using Single Molecule Real Time Sequencing (SMRT) 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.

Coccidioidomycosis in Northern Arizona: an Investigation of the Host, Pathogen, and Environment Using a Disease Triangle Approach

“…Raw reads for 60 previously published C. posadasii samples representing the Caribbean, Arizona, Texas/Mexico/South America clades ( 41 ), and the seven new clinical isolates were aligned (82.72% or 23,336,819 bases) to reference the C. posadasii strain Silveira genome, accession number PRJNA494320 ( 89 ). The Northern Arizona Sequencing Pipeline ( 90 ) was used to build an SNP (single nucleotide polymorphism) matrix and map 270,853 SNPs, which were used to identify the best substitution model TVM+F+ASC+R5 using 1,000 bootstrap iterations and build a maximum likelihood tree using IQ-TREE version 1.6.1, based on 152,663 parsimony-informative SNPs ( 91 ).…”

The WOPR family protein Ryp1 is a key regulator of gene expression, development, and virulence in the thermally dimorphic fungal pathogen Coccidioides posadasii

“…HcG217B, HcG217B_anno, and HcG217B_GenBank give the GSC systematic gene name and annotation (from [ 50 ]) and GenBank accession for the InParanoid-mapped HcG217B ortholog. Cp_new_GenBank gives the GenBank accession for the corresponding gene in the newly available Cp Silveira assembly and annotation (BioProject PRJNA664774) [ 51 ]. Class indicates the differential expression pattern, as referenced in the results and discussion sections.…”

Coccidioides Species: A Review of Basic Research: 2022

“…However, some of the predicted contigs were very similar in length and they might not be resolved by electrophoresis. Subsequent more-complete studies have shown that C. posadasii Silvera has six chromosomes [ 118 , 119 ]. The size of gene families in Onygenales and Eurotiales taxa was compared [ 59 ].…”

“…A chromosomal-level sequence of C. posadasii Silvera has also recently been obtained [ 118 , 119 ]. This sequencing project relied heavily on Single Molecule Real-Time Sequencing to obtain the sequence of long reads as well as short-read sequencing to improve the quality of chromosomal sequence.…”