Wang Han
Department of Zoology and Stephenson Research & Technology Center, University of Oklahoma, Norman, OK 73019, USA.
Genetica. 2009 May;136(1):149-61. doi: 10.1007/s10709-008-9328-9. Epub 2008 Oct 14.
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.
Bmal1（脑和肌肉芳香烃受体核转运蛋白样1）基因是关键的生物钟基因。四足动物还有第二个Bmal基因，即Bmal2。果蝇只有一个bmal1/周期基因。对五个硬骨鱼基因组序列进行查询，并结合系统发育分析和剪接位点分析发现，斑马鱼有两个bmal1基因，bmal1a和bmal1b，以及bmal2a；日本河豚（红鳍东方鲀）、黑点绿河豚（暗斑叉鼻鲀）和日本青鳉各自有两个bmal2基因，bmal2a和bmal2b，以及bmal1a；三刺鱼有bmal1a和bmal2b。共线性分析进一步表明，斑马鱼的bmal1a/bmal1b，以及河豚、暗斑叉鼻鲀和青鳉的bmal2a/bmal2b是古老的重复基因。尽管这四种鱼类bmal重复基因的dN/dS比率均<1，表明它们一直处于纯化选择之下，但 Tajima 相对速率检验表明，河豚、暗斑叉鼻鲀和青鳉的bmal2a/bmal2b具有不对称的进化速率，这表明这些重复基因中的一个经历了正选择或功能限制的放松。这些结果支持了这样一种观点，即硬骨鱼的bmal基因源自鱼类特有的基因组复制（FSGD），复制后的分化解析导致不同鱼类保留了不同的古老bmal重复基因，这可能塑造了硬骨鱼复杂计时机制的进化。
