title: Phylogenetic analysis of zebrafish basic helix-loop-helix transcription factors.
abstract: The basic helix-loop-helix (bHLH) proteins play important regulatory roles in eukaryotic developmental processes including neurogenesis, myogenesis, hematopoiesis, sex determination, and gut development. Zebrafish is a good model organism for developmental biology. In this study, we identified 139 bHLH genes encoded in the zebrafish genome. Phylogenetic analyses revealed that zebrafish has 58, 29, 21, 5, 19, and 5 bHLH members in groups A, B, C, D, E, and F, respectively, while 2 members were classified as "orphan." A comparison between zebrafish and human bHLH repertoires suggested that both organisms have a certain number of specific bHLH members. Eight zebrafish bHLH genes were found to have multiple coding regions in the genome. Two of these, Bmal1 and MITF, are good anchor genes for identification of fish-specific whole-genome duplication events in comparison with mouse and chicken genomes. The present study provides useful information for future studies on gene family evolution and vertebrate development.
authors.affiliation: Department of Biotechnology, School of Food and Biological Engineering, Jiangsu University, 301 Xuefu Road, Zhenjiang, 212013, People's Republic of China. ywang@ujs.edu.cn
authors.forename: Yong
authors.initials: Y
authors.lastname: Wang
authors.forename: Keping
authors.initials: K
authors.lastname: Chen
authors.forename: Qin
authors.initials: Q
authors.lastname: Yao
authors.forename: Xiaodong
authors.initials: X
authors.lastname: Zheng
authors.forename: Zhe
authors.initials: Z
authors.lastname: Yang
mesh_terms: D056930:ARNTL Transcription Factors; D000595:Amino Acid Sequence; D000818:Animals; D051792:Basic Helix-Loop-Helix Proteins / Q000235:genetics; D002645:Chickens; D002875:Chromosomes; D030541:Databases, Genetic; D019143:Evolution, Molecular; D018257:Helix-Loop-Helix Motifs / Q000235:genetics*; D051379:Mice; D051739:Microphthalmia-Associated Transcription Factor / Q000235:genetics; D008957:Models, Genetic; D010802:Phylogeny; D016415:Sequence Alignment; D020539:Sequence Analysis, Protein; D014157:Transcription Factors / Q000737:chemistry / Q000235:genetics*; D015027:Zebrafish / Q000235:genetics*; D029961:Zebrafish Proteins / Q000737:chemistry / Q000235:genetics
chemical_list: D056930:ARNTL Transcription Factors; D051792:Basic Helix-Loop-Helix Proteins; D051739:Microphthalmia-Associated Transcription Factor; D014157:Transcription Factors; D029961:Zebrafish Proteins; C538960:BMAL1 protein, human; C538961:Bmal1 protein, mouse