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These acclimatizations are triggered by short photoperiod and orchestrated by the hypothalamus. Key mechanisms of long\u2010term photoperiodic acclimatizations have partly been described, but specific mechanisms that acutely control torpor remain incomplete. Here, we performed comparative transcriptome analysis on hypothalamus of normometabolic hamsters in their summer\u2010 and winter\u2010like state to enable us to identify changes in gene expression during photoperiodic acclimations. Comparing nontorpid and torpid hamsters may also be able to pin down mechanisms relevant for torpor control. A <jats:italic>de\u2009novo<\/jats:italic> assembled transcriptome of the hypothalamus was generated from hamsters acclimated to long photoperiod or to short photoperiod. The hamsters were sampled either during long photoperiod normothermia, short photoperiod normothermia, or short photoperiod\u2010induced spontaneous torpor with a body temperature of 24.6\u2009\u00b1\u20091.0\u2009\u00b0C, or. The mRNA\u2010seq analysis revealed that 32 and 759 genes were differentially expressed during photoperiod or torpor, respectively. Biological processes were not enriched during photoperiodic acclimatization but were during torpor, where transcriptional and metabolic processes were reinforced. Most extremely regulated genes (those genes with |log2(FC)|\u2009&gt;\u20092.0 and padj\u2009&lt;\u20090.05 of a pairwise group comparison) underpinned the role of known key players in photoperiodic comparison, but these genes exhibit adaptive and protective adjustments during torpor. Targeted analyses of genes from potentially involved hypothalamic systems identified gene regulation of previously described torpor\u2010relevant systems and a potential involvement of glucose transport.<\/jats:p>","DOI":"10.1002\/2211-5463.13350","type":"journal-article","created":{"date-parts":[[2021,12,11]],"date-time":"2021-12-11T10:00:32Z","timestamp":1639216832000},"page":"443-459","update-policy":"https:\/\/doi.org\/10.1002\/crossmark_policy","source":"Crossref","is-referenced-by-count":17,"title":["Comparative transcriptomics of the Djungarian hamster hypothalamus during short photoperiod acclimation and spontaneous torpor"],"prefix":"10.1002","volume":"12","author":[{"ORCID":"https:\/\/orcid.org\/0000-0001-7426-2546","authenticated-orcid":false,"given":"Elena","family":"Haugg","sequence":"first","affiliation":[{"name":"Institute of Neurobiology Ulm University Germany"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-9612-6668","authenticated-orcid":false,"given":"Janus","family":"Borner","sequence":"additional","affiliation":[{"name":"Institute of Evolutionary Ecology and Conservation Genomics Ulm University Germany"},{"name":"Sackler Institute for Comparative Genomics American Museum of Natural History New York NY USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-7963-4553","authenticated-orcid":false,"given":"Victoria","family":"Diedrich","sequence":"additional","affiliation":[{"name":"Institute of Neurobiology Ulm University Germany"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-3048-0618","authenticated-orcid":false,"given":"Annika","family":"Herwig","sequence":"additional","affiliation":[{"name":"Institute of Neurobiology Ulm University Germany"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"311","published-online":{"date-parts":[[2021,12,20]]},"reference":[{"key":"e_1_2_11_2_1","doi-asserted-by":"publisher","DOI":"10.1007\/BF00345511"},{"key":"e_1_2_11_3_1","first-page":"99","volume-title":"Endokrinologie IV: Vortr\u00e4ge im Rahmen des Projekts \u201cZeitstrukturen endokriner Systeme\u201d. 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