SCIENCE CHINA Life Sciences © Science China Press and Springer-Verlag Berlin Heidelberg 2010 life.scichina.com www.springerlink.com *Corresponding author (email: clad@ihb.ac.cn )  RESEARCH PAPER  February 2010 Vol.53 No.2: 257–266 doi: 10.1007/s11427-010-0025-4 Olfactory receptor gene family evolution in stickleback and medaka fishes CHEN Ming 1,2 , PENG ZuoGang 1 & HE ShunPing 1* 1 Laboratory of Fish Phylogenetics and Biogeography, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China; 2 Graduate University of Chinese Academy of Sciences, Beijing 100039, China Received July 20, 2009; accepted August 20, 2009 Interaction of olfactory receptor (OR) genes with environmental odors is regarded as the first step of olfaction. In this study, OR genes of two fish, medaka (Oryzias latipes) and stickleback (Gasterosteus aculeatus), were identified and an evolutional analysis was conducted. The selection pressure of different TM regions and complete coding region were compared. Three TM regions (TM4, TM5 and TM6) were found to have higher average Ka/Ks values, which might be partly caused by positive se- lection as suggested by subsequent positive selection analysis. Further analysis showed that many PTSs overlap, or are adja- cent to previously deduced binding sites in mammals. These results support the hypothesis that binding sites of fish OR genes may evolved under positive selection. olfactory receptor, positive selection, binding site Citation: Chen M, Peng Z G, He S P. Olfactory receptor gene family evolution in stickleback and medaka fishes. Sci China Life Sci, 2010, 53: 257 – 266, doi: 10.1007/s11427-010-0025-4 Olfaction enable vertebrates to identify foods, mates and avoid danger. Olfaction is initiated by the interaction of en- vironmental ligands with the olfactory Receptors (OR) ex- pressed in sensory neurons of the olfactory epithelia in nasal cavities [1,2]. OR genes were first found in rats [3] and be- long to the rhodopsin-like G-protein coupled receptor (GPCR) gene hyper-family characterized by seven helical TM domains. OR genes constitute one of the largest gene families in the vertebrate genomes, comprising ~1000 genes in the mammalian genome [4–7] and ~100 members in the fish genome [8–10]. Studies of OR genes in mammal genomes showed that human OR genes have different patterns from that of mice and dogs. Niimura and Nei [7] identified 388 potential functional genes and 414 pseudogenes in humans, whereas they identified 1037 functional genes and 354 pseudogenes in mice [11]. The total number of functional genes in the mouse genome is ~2.7 times of that in the human genome. Furthermore, there are ~75% functional genes in the mouse genome, which is larger than that of the human genome at 48%. There are also more functional OR genes in the dog genome than in the human genome, and the percentage of functional genes in the former, >80% is also significantly larger than in the latter, 48% [12,13]. These differences are consistent with the more sensitive olfaction in mouse and dogs. It was reported that the loss of OR genes coincides with the acquisition of full trichromatic vision in primates, suggesting that full trichromatic vision diminished the need for olfaction for survival [14]. These results showed that olfaction ability may have a positive correlation with the number of functional OR genes in mammals [15]. In the fish genomes, there are relatively fewer (~100) OR genes, as compared with that in the mammalian genome. However, the fish OR genes are more divergent than mammalian OR genes [10]. The odor specialty of OR proteins is determined by relatively fewer amino acids, usually called binding sites