TY - JOUR
T1 - A chromosomal-level reference genome of the widely utilized Coccidioides posadasii laboratory strain "Silveira"
AU - De Melo Teixeira, Marcus
AU - Stajich, Jason E.
AU - Sahl, Jason W.
AU - Thompson, George R.
AU - Brem, Rachel B.
AU - Dubin, Claire A.
AU - Blackmon, Austin V.
AU - Mead, Heather L.
AU - Keim, Paul
AU - Barker, Bridget M.
N1 - Funding Information:
Funding to PK Arizona Biomedical Research Commission/Arizona Department of Health Services 18-198851. BMB was partly funded by National Institutes of Health/National Institute of Allergy and Infectious Disease R21AI28536-01AI. JES is a Canadian Institute For Advanced Research Fellow in the program Fungal Kingdom: Threats and Opportunities and was supported by the University of California Multicampus Research Programs and Initiatives grants MRP-17-454959 “UC Valley Fever Research Initiative” and VFR-19-633952 “Investigating fundamental gaps in Valley Fever knowledge” and United States Department of Agriculture— National Institute of Food and Agriculture Hatch Project CA-R-PPA-5062-H.
Publisher Copyright:
© 2022 Genetics Society of America. All rights reserved.
PY - 2022/4
Y1 - 2022/4
N2 - 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.
AB - 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.
KW - coccidioidomycosis
KW - funannotate
KW - fungal genomes
KW - human fungal pathogen
KW - long-read sequencing
KW - reference genome
KW - valley fever
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U2 - 10.1093/g3journal/jkac031
DO - 10.1093/g3journal/jkac031
M3 - Article
C2 - 35137016
AN - SCOPUS:85128245226
SN - 2160-1836
VL - 12
JO - G3: Genes, Genomes, Genetics
JF - G3: Genes, Genomes, Genetics
IS - 4
M1 - jkac031
ER -