Proteogenomic Re-Annotation of Coccidioides posadasii Strain Silveira

Natalie M. Mitchell, Andrew L. Sherrard, Surendra Dasari, Dewey Magee, Thomas E. Grys, Douglas Lake

Research output: Contribution to journalArticle

6 Citations (Scopus)

Abstract

The aims of this study are to provide protein-based evidence upon which to reannotate the genome of Coccidiodes posadasii, one of two closely related species of Coccidioides, a dimorphic fungal pathogen that causes coccidioidomycosis, also called Valley fever. Proteins present in lysates and filtrates of in vitro grown mycelia and parasitic phase spherules from C. posadasii strain Silveira are analyzed using a GeLC-MS/MS method. Acquired spectra are processed with a proteogenomics workflow comprising a Silveira proteome database, a six-frame translation of the Silveira genome and an ab initio gene prediction tool prior to validation against published ESTs. This study provides evidence for 837 genes expressed at the protein level, of which 169 proteins (20.2%) are putative proteins and 103 (12.3%) are not annotated in the Silveira genome. Additionally, 275 novel peptides are derived from intragenic regions of the genome and 13 from intergenic regions, resulting in 172 gene refinements. Additionally, we are the first group to report translationally active retrotransposon elements in a Coccidioides spp. Our study reveals that the currently annotated genome of C. posadasii str. Silveira needs refinement, which is likely to be the case for many nonmodel organisms.

Original languageEnglish (US)
Article number1700173
JournalProteomics
Volume18
Issue number1
DOIs
StatePublished - Jan 1 2018

Fingerprint

Coccidioides
Genes
Genome
Coccidioidomycosis
Proteins
Retroelements
Intergenic DNA
Workflow
Mycelium
Expressed Sequence Tags
Proteome
Proteogenomics
Proteomics
Databases
Pathogens
Peptides

Keywords

  • Coccidioides
  • coccidioidomycosis
  • genomics
  • proteogenomics
  • valley fever

ASJC Scopus subject areas

  • Biochemistry
  • Molecular Biology

Cite this

Proteogenomic Re-Annotation of Coccidioides posadasii Strain Silveira. / Mitchell, Natalie M.; Sherrard, Andrew L.; Dasari, Surendra; Magee, Dewey; Grys, Thomas E.; Lake, Douglas.

In: Proteomics, Vol. 18, No. 1, 1700173, 01.01.2018.

Research output: Contribution to journalArticle

Mitchell, Natalie M. ; Sherrard, Andrew L. ; Dasari, Surendra ; Magee, Dewey ; Grys, Thomas E. ; Lake, Douglas. / Proteogenomic Re-Annotation of Coccidioides posadasii Strain Silveira. In: Proteomics. 2018 ; Vol. 18, No. 1.
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