{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,8,27]],"date-time":"2026-08-27T18:43:22Z","timestamp":1787856202533,"version":"build-2784847793"},"reference-count":71,"publisher":"Oxford University Press (OUP)","issue":"3","funder":[{"DOI":"10.13039\/100005420","name":"Arctic-Yukon-Kuskokwim Sustainable Salmon Initiative","doi-asserted-by":"publisher","award":["AC-2204"],"award-info":[{"award-number":["AC-2204"]}],"id":[{"id":"10.13039\/100005420","id-type":"DOI","asserted-by":"publisher"}]},{"name":"ADF&G Fish Pathology Laboratory"},{"DOI":"10.13039\/100008144","name":"ADF&G","doi-asserted-by":"publisher","award":["NA22NMF4380212"],"award-info":[{"award-number":["NA22NMF4380212"]}],"id":[{"id":"10.13039\/100008144","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2026,8,27]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:sec>\n                    <jats:title>Objective<\/jats:title>\n                    <jats:p>We compared differentially expressed genes in Chinook Salmon Oncorhynchus tshawytscha with three divergent Ichthyophonus statuses (undetected, subclinical infections, or clinical disease; n = 100) to investigate associated transcriptomic responses. Disease associated with the fish parasite Ichthyophonus sp. was first diagnosed in adult Chinook Salmon from the Yukon River in the late 1980s and has subsequently been implicated in premature host mortality.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Methods<\/jats:title>\n                    <jats:p>Chinook Salmon tissue sample collections and Ichthyophonus infection data were leveraged from a multi-agency collaboration during summer 2022 at three locations along the main-stem Yukon River that spanned nearly 2,000\u2005km of freshwater migration (lower, middle, and upper river). We sequenced the transcriptome and compared this to infection status based on routine diagnostic procedures.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Results<\/jats:title>\n                    <jats:p>Among the 17,569 genes for which messenger RNA was detected, we identified a transcription signature in the skeletal muscle that was associated with Ichthyophonus infections and included 53 differentially expressed genes. The differentially expressed genes and their pathways included those known for involvement in immune functions, energy synthesis, cellular breakdown, and reproduction\u2014all processes that are known to be influenced by senescence during spawning migrations.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Conclusions<\/jats:title>\n                    <jats:p>Results demonstrate a clear transcriptional difference between diseased fish (clinical disease group) and those in which Ichthyophonus was undetected, including identifying candidate markers for infection in this population. These results provide a foundation for development of nonlethal biomarkers to evaluate potential Ichthyophonus infections in Chinook Salmon based on gene transcription, protein products, or gene variants (e.g., polymorphisms).<\/jats:p>\n                  <\/jats:sec>","DOI":"10.1093\/jahafs\/vsag007","type":"journal-article","created":{"date-parts":[[2026,6,29]],"date-time":"2026-06-29T17:46:43Z","timestamp":1782755203000},"page":"87-106","source":"Crossref","is-referenced-by-count":0,"title":["Transcriptional changes in wild Yukon River Chinook Salmon associated with\n                    <i>Ichthyophonus<\/i>\n                    infections"],"prefix":"10.1093","volume":"38","author":[{"given":"Lizabeth","family":"Bowen","sequence":"first","affiliation":[{"name":"U.S. Geological Survey, Western Ecological Research Center , Davis, California ,","place":["USA"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-7139-5981","authenticated-orcid":false,"given":"Vanessa R","family":"von Biela","sequence":"additional","affiliation":[{"name":"U.S. Geological Survey, Alaska Science Center , Anchorage, Alaska ,","place":["USA"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-0384-5159","authenticated-orcid":false,"given":"Jayde A","family":"Ferguson","sequence":"additional","affiliation":[{"name":"Alaska Department of Fish and Game, Division of Commercial Fisheries, Fish Pathology Section , Anchorage, Alaska ,","place":["USA"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Shannon C","family":"Waters","sequence":"additional","affiliation":[{"name":"U.S. Geological Survey, Western Ecological Research Center , Davis, California ,","place":["USA"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-4747-4265","authenticated-orcid":false,"given":"Amy M","family":"Regish","sequence":"additional","affiliation":[{"name":"U.S. Geological Survey, Eastern Ecological Science Center, S.O. Conte Research Laboratory , Turners Falls, Massachusetts ,","place":["USA"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-3327-8995","authenticated-orcid":false,"given":"Michael P","family":"Carey","sequence":"additional","affiliation":[{"name":"U.S. Geological Survey, Alaska Science Center , Anchorage, Alaska ,","place":["USA"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Zachary","family":"Liller","sequence":"additional","affiliation":[{"name":"Alaska Department of Fish and Game, Division of Commercial Fisheries , Arctic-Yukon-Kuskokwim Region, Anchorage, Alaska ,","place":["USA"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Morag","family":"Clinton","sequence":"additional","affiliation":[{"name":"Sitka Sound Science Center , Sitka, Alaska ,","place":["USA"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Paul 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