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Reliable analyses using quantitative real-time PCR (qRT-PCR) for answering these scientific questions is heavily dependent on reliable reference genes (RGs). In this study, we evaluated stability of thirteen candidate RGs in qRT-PCR for different developmental stages and tissues of amphioxus by four independent (geNorm, NormFinder, BestKeeper and deltaCt) and one comparative algorithms (RefFinder). The results showed that the top two stable RGs were the following: (1)<jats:italic>S20<\/jats:italic>and<jats:italic>18<\/jats:italic>\u2009<jats:italic>S<\/jats:italic>in thirteen developmental stages, (2)<jats:italic>EF1A<\/jats:italic>and<jats:italic>ACT<\/jats:italic>in seven normal tissues, (3)<jats:italic>S20<\/jats:italic>and<jats:italic>L13<\/jats:italic>in both intestine and hepatic caecum challenged with lipopolysaccharide (LPS), and (4)<jats:italic>S20<\/jats:italic>and<jats:italic>EF1A<\/jats:italic>in gill challenged with LPS. The expression profiles of two target genes (<jats:italic>EYA<\/jats:italic>and<jats:italic>HHEX<\/jats:italic>) in thirteen developmental stages were used to confirm the reliability of chosen RGs. This study identified optimal RGs that can be used to accurately measure gene expression under these conditions, which will benefit evolutionary and functional genomics studies in amphioxus.<\/jats:p>","DOI":"10.1038\/srep37549","type":"journal-article","created":{"date-parts":[[2016,11,21]],"date-time":"2016-11-21T10:12:19Z","timestamp":1479723139000},"update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":33,"title":["Selection of reliable reference genes for normalization of quantitative RT-PCR from different developmental stages and tissues in amphioxus"],"prefix":"10.1038","volume":"6","author":[{"given":"Qi-Lin","family":"Zhang","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Qian-Hua","family":"Zhu","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Xin","family":"Liao","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Xiu-Qiang","family":"Wang","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Tao","family":"Chen","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Han-Ting","family":"Xu","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Juan","family":"Wang","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Ming-Long","family":"Yuan","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jun-Yuan","family":"Chen","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"297","published-online":{"date-parts":[[2016,11,21]]},"reference":[{"key":"BFsrep37549_CR1","doi-asserted-by":"publisher","first-page":"986","DOI":"10.1101\/gr.6.10.986","volume":"6","author":"CA Heid","year":"1996","unstructured":"Heid, C. 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