title: Origin and diversification of the basic helix-loop-helix gene family in metazoans: insights from comparative genomics.
abstract: BACKGROUND
  Molecular and genetic analyses conducted in model organisms such as Drosophila and vertebrates, have provided a wealth of information about how networks of transcription factors control the proper development of these species. Much less is known, however, about the evolutionary origin of these elaborated networks and their large-scale evolution. Here we report the first evolutionary analysis of a whole superfamily of transcription factors, the basic helix-loop-helix (bHLH) proteins, at the scale of the whole metazoan kingdom.
  
  
  RESULTS
  We identified in silico the putative full complement of bHLH genes in the sequenced genomes of 12 different species representative of the main metazoan lineages, including three non-bilaterian metazoans, the cnidarians Nematostella vectensis and Hydra magnipapillata and the demosponge Amphimedon queenslandica. We have performed extensive phylogenetic analyses of the 695 identified bHLHs, which has allowed us to allocate most of these bHLHs to defined evolutionary conserved groups of orthology.
  
  
  CONCLUSIONS
  Three main features in the history of the bHLH gene superfamily can be inferred from these analyses: (i) an initial diversification of the bHLHs has occurred in the pre-Cambrian, prior to metazoan cladogenesis; (ii) a second expansion of the bHLH superfamily occurred early in metazoan evolution before bilaterians and cnidarians diverged; and (iii) the bHLH complement during the evolution of the bilaterians has been remarkably stable. We suggest that these features may be extended to other developmental gene families and reflect a general trend in the evolution of the developmental gene repertoires of metazoans.
authors.affiliation: Evolution et Développement des protostomiens, Centre de Génétique Moléculaire- UPR 2167 CNRS, Gif-sur-Yvette Cedex, France. Elena.Simionato@cgm.cnrs-gif.fr <Elena.Simionato@cgm.cnrs-gif.fr>
authors.forename: Elena
authors.initials: E
authors.lastname: Simionato
authors.forename: Valérie
authors.initials: V
authors.lastname: Ledent
authors.forename: Gemma
authors.initials: G
authors.lastname: Richards
authors.forename: Morgane
authors.initials: M
authors.lastname: Thomas-Chollier
authors.forename: Pierre
authors.initials: P
authors.lastname: Kerner
authors.forename: David
authors.initials: D
authors.lastname: Coornaert
authors.forename: Bernard M
authors.initials: BM
authors.lastname: Degnan
authors.forename: Michel
authors.initials: M
authors.lastname: Vervoort
mesh_terms: D000595:Amino Acid Sequence; D000818:Animals; D019143:Evolution, Molecular; D005796:Genes; D023281:Genomics; D018257:Helix-Loop-Helix Motifs / Q000235:genetics*; D006801:Humans; D010802:Phylogeny; D017386:Sequence Homology, Amino Acid