2
views
0
recommends
+1 Recommend
0 collections
    0
    shares
      • Record: found
      • Abstract: not found
      • Article: not found

      Proteogenomic Re-Annotation of Coccidioides posadasii Strain Silveira

      Read this article at

      ScienceOpenPublisherPubMed
      Bookmark
          There is no author summary for this article yet. Authors can add summaries to their articles on ScienceOpen to make them more accessible to a non-specialist audience.

          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.

          Related collections

          Author and article information

          Journal
          PROTEOMICS
          Proteomics
          Wiley
          16159853
          January 2018
          January 2018
          December 14 2017
          : 18
          : 1
          : 1700173
          Affiliations
          [1 ]School of Life Sciences; Mayo Clinic Collaborative Research Building; Arizona State University; Scottsdale AZ USA
          [2 ]Department of Health Sciences Research; Mayo Clinic; Rochester MN USA
          [3 ]Center for Personalized Diagnostics; Biodesign Institute; Arizona State University; Tempe AZ USA
          [4 ]Department of Laboratory Medicine and Pathology; Mayo Clinic; Phoenix AZ USA
          Article
          10.1002/pmic.201700173
          29130603
          a97d3f0e-b18b-4bc6-98e0-21269facfd8a
          © 2017

          http://doi.wiley.com/10.1002/tdm_license_1.1

          http://onlinelibrary.wiley.com/termsAndConditions#vor

          History

          Comments

          Comment on this article