{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,10,22]],"date-time":"2025-10-22T03:10:40Z","timestamp":1761102640552,"version":"build-2065373602"},"reference-count":29,"publisher":"Wiley","issue":"1","license":[{"start":{"date-parts":[[2017,12,14]],"date-time":"2017-12-14T00:00:00Z","timestamp":1513209600000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/onlinelibrary.wiley.com\/termsAndConditions#vor"}],"funder":[{"DOI":"10.13039\/100000871","name":"Mayo Clinic","doi-asserted-by":"publisher","id":[{"id":"10.13039\/100000871","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100008335","name":"Arizona Biomedical Research Commission","doi-asserted-by":"publisher","award":["ADH16\u2010162513"],"award-info":[{"award-number":["ADH16\u2010162513"]}],"id":[{"id":"10.13039\/100008335","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":["analyticalsciencejournals.onlinelibrary.wiley.com"],"crossmark-restriction":true},"short-container-title":["Proteomics"],"published-print":{"date-parts":[[2018,1]]},"abstract":"<jats:title>Abstract<\/jats:title><jats:p>The aims of this study are to provide protein\u2010based evidence upon which to reannotate the genome of <jats:italic>Coccidiodes posadasii<\/jats:italic>, one of two closely related species of <jats:italic>Coccidioides<\/jats:italic>, 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 <jats:italic>C. posadasii<\/jats:italic> strain Silveira are analyzed using a GeLC\u2010MS\/MS method. Acquired spectra are processed with a proteogenomics workflow comprising a Silveira proteome database, a six\u2010frame 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 <jats:italic>Coccidioides spp<\/jats:italic>. Our study reveals that the currently annotated genome of <jats:italic>C. posadasii<\/jats:italic> str. Silveira needs refinement, which is likely to be the case for many nonmodel organisms.<\/jats:p>","DOI":"10.1002\/pmic.201700173","type":"journal-article","created":{"date-parts":[[2017,11,12]],"date-time":"2017-11-12T08:52:41Z","timestamp":1510476761000},"update-policy":"https:\/\/doi.org\/10.1002\/crossmark_policy","source":"Crossref","is-referenced-by-count":0,"title":["Proteogenomic Re\u2010Annotation of <i>Coccidioides posadasii<\/i> Strain Silveira"],"prefix":"10.1002","volume":"18","author":[{"given":"Natalie M.","family":"Mitchell","sequence":"first","affiliation":[{"name":"School of Life Sciences Mayo Clinic Collaborative Research Building Arizona State University  Scottsdale AZ USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Andrew L.","family":"Sherrard","sequence":"additional","affiliation":[{"name":"School of Life Sciences Mayo Clinic Collaborative Research Building Arizona State University  Scottsdale AZ USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Surendra","family":"Dasari","sequence":"additional","affiliation":[{"name":"Department of Health Sciences Research Mayo Clinic  Rochester MN USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"D. Mitchell","family":"Magee","sequence":"additional","affiliation":[{"name":"Center for Personalized Diagnostics Biodesign Institute Arizona State University  Tempe AZ USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Thomas E.","family":"Grys","sequence":"additional","affiliation":[{"name":"Department of Laboratory Medicine and Pathology Mayo Clinic  Phoenix AZ USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Douglas F.","family":"Lake","sequence":"additional","affiliation":[{"name":"School of Life Sciences Mayo Clinic Collaborative Research Building Arizona State University  Scottsdale AZ USA"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"311","published-online":{"date-parts":[[2017,12,14]]},"reference":[{"key":"e_1_2_8_1_1","doi-asserted-by":"publisher","DOI":"10.1080\/13693780701288070"},{"key":"e_1_2_8_2_1","doi-asserted-by":"publisher","DOI":"10.1073\/pnas.071406098"},{"key":"e_1_2_8_3_1","doi-asserted-by":"publisher","DOI":"10.1101\/gr.103911.109"},{"key":"e_1_2_8_4_1","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pone.0041034"},{"key":"e_1_2_8_5_1","doi-asserted-by":"publisher","DOI":"10.1016\/j.jprot.2010.06.007"},{"key":"e_1_2_8_6_1","doi-asserted-by":"publisher","DOI":"10.1074\/mcp.M200008-MCP200"},{"key":"e_1_2_8_7_1","doi-asserted-by":"publisher","DOI":"10.1080\/07388550701334212"},{"key":"e_1_2_8_8_1","doi-asserted-by":"publisher","DOI":"10.1128\/MCB.19.3.1720"},{"key":"e_1_2_8_9_1","doi-asserted-by":"publisher","DOI":"10.1021\/acs.jproteome.5b01054"},{"key":"e_1_2_8_10_1","doi-asserted-by":"crossref","first-page":"449","DOI":"10.1128\/iai.53.3.449-453.1986","volume":"53","author":"Cox R. A.","year":"1986","journal-title":"Infect. Immun."},{"key":"e_1_2_8_11_1","doi-asserted-by":"crossref","first-page":"2590","DOI":"10.1128\/iai.55.11.2590-2596.1987","volume":"55","author":"Cox R. A.","year":"1987","journal-title":"Infect. Immun."},{"key":"e_1_2_8_12_1","doi-asserted-by":"publisher","DOI":"10.1038\/nbt1329"},{"key":"e_1_2_8_13_1","doi-asserted-by":"publisher","DOI":"10.1093\/nar\/gks1262"},{"key":"e_1_2_8_14_1","doi-asserted-by":"publisher","DOI":"10.1101\/gr.087551.108"},{"key":"e_1_2_8_15_1","doi-asserted-by":"publisher","DOI":"10.1093\/nar\/gkr918"},{"key":"e_1_2_8_16_1","doi-asserted-by":"publisher","DOI":"10.1093\/nar\/gkl200"},{"key":"e_1_2_8_17_1","unstructured":"M. R.Henn S.Sykes S.Young D.Jaffe A.Berlin P.Alvarez J.Butler S.Gnerre M.Grabherr E.Mauceli W.Brockman C.Kodira L.Alarado Q.Zeng M.Crawford C.Antoine K.Devon J. N.Galgiani K.Osborn M. L.Louis C.Nusbaum J.Galagan B.Birren 2007."},{"key":"e_1_2_8_18_1","doi-asserted-by":"publisher","DOI":"10.1093\/bioinformatics\/btn323"},{"key":"e_1_2_8_19_1","doi-asserted-by":"publisher","DOI":"10.1038\/ncomms6277"},{"key":"e_1_2_8_20_1","doi-asserted-by":"publisher","DOI":"10.1021\/pr900360j"},{"key":"e_1_2_8_21_1","doi-asserted-by":"publisher","DOI":"10.1038\/nbt.1754"},{"key":"e_1_2_8_22_1","doi-asserted-by":"publisher","DOI":"10.1093\/nar\/gkv1290"},{"key":"e_1_2_8_23_1","doi-asserted-by":"publisher","DOI":"10.1093\/nar\/gkm286"},{"key":"e_1_2_8_24_1","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pone.0106942"},{"key":"e_1_2_8_25_1","doi-asserted-by":"publisher","DOI":"10.1146\/annurev-micro-092611-150138"},{"key":"e_1_2_8_26_1","doi-asserted-by":"publisher","DOI":"10.3390\/ijms140815348"},{"key":"e_1_2_8_27_1","doi-asserted-by":"crossref","DOI":"10.1128\/microbiolspec.FUNK-0008-2016","volume":"4","author":"Nicolas F. E.","year":"2016","journal-title":"Microbiol. Spectr."},{"key":"e_1_2_8_28_1","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pone.0029425"},{"key":"e_1_2_8_29_1","doi-asserted-by":"publisher","DOI":"10.1186\/s12864-016-3432-5"}],"container-title":["PROTEOMICS"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/api.wiley.com\/onlinelibrary\/tdm\/v1\/articles\/10.1002%2Fpmic.201700173","content-type":"application\/pdf","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/analyticalsciencejournals.onlinelibrary.wiley.com\/doi\/pdf\/10.1002\/pmic.201700173","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2025,10,21]],"date-time":"2025-10-21T13:30:30Z","timestamp":1761053430000},"score":1,"resource":{"primary":{"URL":"https:\/\/analyticalsciencejournals.onlinelibrary.wiley.com\/doi\/10.1002\/pmic.201700173"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2017,12,14]]},"references-count":29,"journal-issue":{"issue":"1","published-print":{"date-parts":[[2018,1]]}},"alternative-id":["10.1002\/pmic.201700173"],"URL":"https:\/\/doi.org\/10.1002\/pmic.201700173","archive":["Portico"],"relation":{},"ISSN":["1615-9853","1615-9861"],"issn-type":[{"type":"print","value":"1615-9853"},{"type":"electronic","value":"1615-9861"}],"subject":[],"published":{"date-parts":[[2017,12,14]]},"assertion":[{"value":"2017-05-11","order":0,"name":"received","label":"Received","group":{"name":"publication_history","label":"Publication History"}},{"value":"2017-12-14","order":3,"name":"published","label":"Published","group":{"name":"publication_history","label":"Publication History"}}],"article-number":"1700173"}}