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Crustaceans represent the second largest group of arthropods with insects being the largest. However, relative to insects, little is known about the nuclear receptors of crustaceans. The aim of this study was to identify putative nuclear receptors from the first assembled genome of a crustacean<jats:italic>Daphnia pulex<\/jats:italic><jats:ext-link xmlns:xlink=\"http:\/\/www.w3.org\/1999\/xlink\" xlink:href=\"http:\/\/wFleaBase.org\" ext-link-type=\"uri\">http:\/\/wFleaBase.org<\/jats:ext-link>. Nuclear receptor expression was evaluated and receptors were subjected to phylogenetic analyses to gain insight into evolution and function.<\/jats:p><\/jats:sec><jats:sec><jats:title>Results<\/jats:title><jats:p>Twenty-five putative nuclear receptors were identified in<jats:italic>D. pulex<\/jats:italic>based on the presence of a conserved DNA-binding domain. All of the nuclear receptor protein sequences contain a highly homologous DNA-binding domain and a less conserved ligand-binding domain with the exception of the NR0A group. These receptors lack a ligand-binding domain. Phylogenetic analysis revealed the presence of all seven receptor subfamilies. The<jats:italic>D. pulex<\/jats:italic>genome contains several nuclear receptors that have vertebrate orthologs. However, several nuclear receptor members that are represented in vertebrates are absent from<jats:italic>D. pulex<\/jats:italic>. Notable absences include receptors of the 1C group (peroxisome proliferators-activated receptors), the 3A group (estrogen receptor), and the 3C group (androgen, progestogen, mineralcorticoid, and glucocorticoid receptors). The<jats:italic>D. pulex<\/jats:italic>genome also contains nuclear receptor orthologs that are present in insects and nematodes but not vertebrates, including putative nuclear receptors within the NR0A group. A novel group of receptors, designated HR97, was identified in<jats:italic>D. pulex<\/jats:italic>that groups with the HR96\/CeNHR8\/48\/DAF12 clade, but forms its own sub-clade. Gene products were detected in adult female<jats:italic>D. pulex<\/jats:italic>for 21 of the 25 receptors.<\/jats:p><\/jats:sec><jats:sec><jats:title>Conclusion<\/jats:title><jats:p>Nuclear receptors are ancient proteins with highly conserved DNA-binding domains. The DNA-binding domains of the nuclear receptors of<jats:italic>D. pulex<\/jats:italic>contain the same degree of conservation that is typically found within nuclear receptors of other species. Most of the receptors identified in<jats:italic>D. pulex<\/jats:italic>have orthologs within the vertebrate and invertebrate lineages examined with the exception of the novel HR97 group and the Dappu-HR10 and potentially the Dappu-HR11 receptors found in<jats:italic>D. pulex<\/jats:italic>. These groups of receptors may harbour functions that are intrinsic to crustacean physiology.<\/jats:p><\/jats:sec>","DOI":"10.1186\/1471-2164-10-500","type":"journal-article","created":{"date-parts":[[2009,10,30]],"date-time":"2009-10-30T11:35:48Z","timestamp":1256902548000},"update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":75,"title":["Annotation, phylogenetics, and expression of the nuclear receptors in Daphnia pulex"],"prefix":"10.1186","volume":"10","author":[{"given":"Susanne A","family":"Thomson","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"William S","family":"Baldwin","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Ying H","family":"Wang","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Gwijun","family":"Kwon","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Gerald A","family":"LeBlanc","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"297","published-online":{"date-parts":[[2009,10,28]]},"reference":[{"issue":"6","key":"2384_CR1","doi-asserted-by":"publisher","first-page":"1429","DOI":"10.1210\/me.2005-0046","volume":"19","author":"RM Evans","year":"2005","unstructured":"Evans RM: The nuclear receptor superfamily: a rosetta stone for physiology. 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