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Abstract Background Members of a class of bHLH transcription factors, namely the <it>hairy</it> (<it>h</it>), <it>Enhancer of split</it> (<it>E(spl)</it>) and <it>hairy</it>-related with YRPW motif (<it>hey</it>) (<it>h/E(spl)/hey</it>) genes are involved in vertebrate somitogenesis and some of them show cycling expression. By sequence comparison, identified orthologues of cycling somitogenesis genes from higher vertebrates do not show an appropriate expression pattern in zebrafish. The zebrafish genomic sequence is not available yet but the genome of <it>Fugu rubripes</it> was recently published. To allow comparative analysis, the currently known Her proteins from zebrafish were used to screen the genomic sequence database of <it>Fugu rubripes</it>. Results 20 <it>h/E(spl)/hey</it>-related genes were identified in <it>Fugu</it>, which is twice the number of corresponding zebrafish genes known so far. A novel class of c-Hairy proteins was identified in the genomes of <it>Fugu</it> and <it>Tetraodon</it>. A screen of the human genome database with the <it>Fugu</it> proteins yielded 10 <it>h/E(spl)/hey</it>-related genes. By analysing the upstream sequences of the <it>c-hairy</it> class genes in zebrafish, <it>Fugu</it> and <it>Tetraodon</it> highly similar sequence stretches were identified that harbour Suppressor of hairless paired binding sites (SPS). This motif was also discovered in the upstream sequences of the <it>her1</it> gene in the examined fish species. Here, the Su(h) sites are separated by longer intervening sequences. Conclusions Our study indicates that not all <it>her</it> homologues in zebrafish have been isolated. Comparison to the human genome suggests a selective duplication of <it>h/E(spl)</it> genes in pufferfish or loss of members of these genes during evolution to the human lineage.</p

Comparative analysis of somitogenesis related genes of the hairy/Enhancer of split class in Fugu and zebrafish