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The biodiversity of coral reef ecosystems depends on a functional symbiosis with photosynthetic dinoflagellates of the highly diverse genus <jats:italic>Symbiodinium<\/jats:italic>, which reside in coral host cells and continuously support their nutrition. The mechanisms underlying symbiont selection to establish a stable endosymbiosis in non-symbiotic juvenile corals are unclear. Here we show for the first time that symbiont selection patterns for larvae of two <jats:italic>Acropora<\/jats:italic> coral species and the model anemone <jats:italic>Aiptasia<\/jats:italic> are similar under controlled conditions. We find that <jats:italic>Aiptasia<\/jats:italic> larvae distinguish between compatible and incompatible symbionts during uptake into the gastric cavity and phagocytosis. Using RNA-Seq, we identify a set of candidate genes potentially involved in symbiosis establishment. Together, our data complement existing molecular resources to mechanistically dissect symbiont phagocytosis in cnidarians under controlled conditions, thereby strengthening the role of <jats:italic>Aiptasia<\/jats:italic> larvae as a powerful model for cnidarian endosymbiosis establishment.<\/jats:p>","DOI":"10.1038\/srep32366","type":"journal-article","created":{"date-parts":[[2016,9,1]],"date-time":"2016-09-01T11:08:27Z","timestamp":1472728107000},"update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":85,"title":["Aiptasia sp. larvae as a model to reveal mechanisms of symbiont selection in cnidarians"],"prefix":"10.1038","volume":"6","author":[{"given":"Iliona","family":"Wolfowicz","sequence":"first","affiliation":[]},{"given":"Sebastian","family":"Baumgarten","sequence":"additional","affiliation":[]},{"given":"Philipp A.","family":"Voss","sequence":"additional","affiliation":[]},{"given":"Elizabeth A.","family":"Hambleton","sequence":"additional","affiliation":[]},{"given":"Christian R.","family":"Voolstra","sequence":"additional","affiliation":[]},{"given":"Masayuki","family":"Hatta","sequence":"additional","affiliation":[]},{"given":"Annika","family":"Guse","sequence":"additional","affiliation":[]}],"member":"297","published-online":{"date-parts":[[2016,9,1]]},"reference":[{"key":"BFsrep32366_CR1","unstructured":"Muscatine, L. 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