title: Selection of reliable reference genes for normalization of quantitative RT-PCR from different developmental stages and tissues in amphioxus.
abstract: Amphioxus is a closest living proxy to the ancestor of cephalochordates with vertebrates, and key animal for novel understanding in the evolutionary origin of vertebrate body plan, genome, tissues and immune system. 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) S20 and 18 S in thirteen developmental stages, (2) EF1A and ACT in seven normal tissues, (3) S20 and L13 in both intestine and hepatic caecum challenged with lipopolysaccharide (LPS), and (4) S20 and EF1A in gill challenged with LPS. The expression profiles of two target genes (EYA and HHEX) 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.
authors.affiliation: Evo-devo Institute, School of Life Sciences, Nanjing University, Nanjing 210008, China.
authors.forename: Qi-Lin
authors.initials: QL
authors.lastname: Zhang
authors.affiliation: BGI-Shenzhen, Shenzhen, 518000, China.
authors.forename: Qian-Hua
authors.initials: QH
authors.lastname: Zhu
authors.affiliation: Evo-devo Institute, School of Life Sciences, Nanjing University, Nanjing 210008, China.
authors.forename: Xin
authors.initials: X
authors.lastname: Liao
authors.affiliation: Evo-devo Institute, School of Life Sciences, Nanjing University, Nanjing 210008, China.
authors.forename: Xiu-Qiang
authors.initials: XQ
authors.lastname: Wang
authors.affiliation: BGI-Shenzhen, Shenzhen, 518000, China.
authors.forename: Tao
authors.initials: T
authors.lastname: Chen
authors.affiliation: Evo-devo Institute, School of Life Sciences, Nanjing University, Nanjing 210008, China.
authors.forename: Han-Ting
authors.initials: HT
authors.lastname: Xu
authors.affiliation: State Key Laboratory of Grassland Agro-Ecosystems, College of Pastoral Agricultural Science and Technology, Lanzhou University, Lanzhou 730020, China.
authors.forename: Juan
authors.initials: J
authors.lastname: Wang
authors.affiliation: State Key Laboratory of Grassland Agro-Ecosystems, College of Pastoral Agricultural Science and Technology, Lanzhou University, Lanzhou 730020, China.
authors.forename: Ming-Long
authors.initials: ML
authors.lastname: Yuan
authors.affiliation: Evo-devo Institute, School of Life Sciences, Nanjing University, Nanjing 210008, China.|Nanjing Institute of Geology and Paleontology, Nanjing 210008, China.
authors.forename: Jun-Yuan
authors.initials: JY
authors.lastname: Chen
mesh_terms: D000465:Algorithms; D000818:Animals; D017931:DNA Primers / Q000378:metabolism; D020869:Gene Expression Profiling; D018507:Gene Expression Regulation, Developmental / Q000187:drug effects; D064175:Lancelets / Q000196:embryology* / Q000235:genetics*; D008070:Lipopolysaccharides / Q000494:pharmacology; D009928:Organ Specificity / Q000187:drug effects / Q000235:genetics; D012015:Reference Standards; D015203:Reproducibility of Results; D020133:Reverse Transcriptase Polymerase Chain Reaction / Q000379:methods* / Q000592:standards*; D012984:Software
chemical_list: D017931:DNA Primers; D008070:Lipopolysaccharides