Comparative analysis of teleost fish genomes reveals preservation of different ancient clock duplicates in different fishes

摘要: Clock (Circadian locomotor output cycle kaput) was the first vertebrate circadian clock gene identified in a mouse forward genetics mutagenesis screen. It encodes bHLH-PAS protein that is highly conserved throughout evolution. Tetrapods also have second gene, Clock2 or Npas2 (Neuronal PAS domain 2). Conversely, fruit fly, an invertebrate, has only one gene. Interrogation of five teleost fish genome databases revealed zebrafish and Japanese pufferfish (fugu) each three genes, whereas green spotted (tetraodon), medaka three-spine stickleback two genes. Phylogenetic splice site analyses indicated fugu clock1 clock1a clock1b clock2; tetraodon but do not clock2. Genome neighborhood analysis further showed clock1a/clock1b zebrafish, ancient duplicate. While dN/dS ratios these duplicates are all <1, indicating purifying selection acted upon them; Tajima relative rate test asymmetric evolutionary rates, implicating been under positive relaxed functional constraint. These results support view genes were generated from genome-wide duplication, differential loss after duplication resulted retention different fishes, which could contributed to evolution distinct mechanisms.