Comparative genomic analysis of teleost fish bmal genes

• Published in: Genetica Vol. 136; no. 1; pp. 149 - 161
• Main Author: Wang, Han
• Format: Journal Article
• Language: English
• Published: Dordrecht Dordrecht : Springer Netherlands 01.05.2009; Springer Netherlands; Springer Nature B.V
• Subjects: Animal Genetics and Genomics; Animals; Base Sequence; Biomedical and Life Sciences; brain; circadian rhythm; Circadian Rhythm - genetics; Comparative Genomic Hybridization; Danio rerio; Drosophila; evolution; Evolution, Molecular; Evolutionary Biology; Fish; Fishes; Fishes - genetics; Freshwater; Fugu; Gene Duplication; genes; genetics; Genome; genomics; Human Genetics; Life Sciences; Marine; Microbial Genetics and Genomics; Molecular Sequence Data; nucleotide sequences; Oryzias latipes; Phylogeny; Plant Genetics and Genomics; RNA Splice Sites; Takifugu; Teleostei; Tetraodon; Japan; Conserved synteny; Differential gene loss; Ratio of nonsynonymous to synonymous substitutions and relative evolutionary rates; Genome duplication; Circadian clocks
• ISSN: 0016-6707; 1573-6857; 1573-6857
• DOI: 10.1007/s10709-008-9328-9

Bmal1 (Brain and muscle ARNT like 1) gene is a key circadian clock gene. Tetrapods also have the second Bmal gene, Bmal2. Fruit fly has only one bmal1/cycle gene. Interrogation of the five teleost fish genome sequences coupled with phylogenetic and splice site analyses found that zebrafish have two bmal1 genes, bmal1a and bmal1b, and bmal2a; Japanese pufferfish (fugu), green spotted pufferfish (tetraodon) and Japanese medaka fish each have two bmal2 genes, bmal2a and bmal2b, and bmal1a; and three-spine stickleback have bmal1a and bmal2b. Syntenic analysis further indicated that zebrafish bmal1a/bmal1b, and fugu, tetraodon and medaka bmal2a/bmal2b are ancient duplicates. Although the dN/dS ratios of these four fish bmal duplicates are all <1, implicating they have been under purifying selection, the Tajima relative rate test showed that fugu, tetraodon and medaka bmal2a/bmal2b have asymmetric evolutionary rates, suggesting that one of these duplicates have been subject to positive selection or relaxed functional constraint. These results support the notion that teleost fish bmal genes were derived from the fish-specific genome duplication (FSGD), divergent resolution following the duplication led to retaining different ancient bmal duplicates in different fishes, which could have shaped the evolution of the complex teleost fish timekeeping mechanisms.