title: Accelerated evolution of 3'avian FOXE1 genes, and thyroid and feather specific expression of chicken FoxE1.
abstract: BACKGROUND
  The forkhead transcription factor gene E1 (FOXE1) plays an important role in regulation of thyroid development, palate formation and hair morphogenesis in mammals. However, avian FOXE1 genes have not been characterized and as such, codon evolution of FOXE1 orthologs in a broader evolutionary context of mammals and birds is not known.
  
  
  RESULTS
  In this study we identified the avian FOXE1 gene in chicken, turkey and zebra finch, all of which consist of a single exon. Chicken and zebra finch FOXE1 are uniquely located on the sex-determining Z chromosome. In situ hybridization shows that chicken FOXE1 is specifically expressed in the developing thyroid. Its expression is initiated at the placode stage and is maintained during the stages of vesicle formation and follicle primordia. Based on this expression pattern, we propose that avian FOXE1 may be involved in regulating the evagination and morphogenesis of thyroid. Chicken FOXE1 is also expressed in growing feathers. Sequence analysis identified two microdeletions in the avian FOXE1 genes, corresponding to the loss of a transferable repression domain and an engrailed homology motif 1 (Eh1) C-terminal to the forkhead domain. The avian FOXE1 proteins exhibit a significant sequence divergence of the C-terminus compared to those of amphibian and mammalian FOXE1. The codon evolution analysis (dN/dS) of FOXE1 shows a significantly increased dN/dS ratio in the avian lineages, consistent with either a relaxed purifying selection or positive selection on a few residues in avian FOXE1 evolution. Further site specific analysis indicates that while relaxed purifying selection is likely to be a predominant cause of accelerated evolution at the 3'-region of avian FOXE1, a few residues might have evolved under positive selection.
  
  
  CONCLUSIONS
  We have identified three avian FOXE1 genes based on synteny and sequence similarity as well as characterized the expression pattern of the chicken FOXE1 gene during development. Our evolutionary analyses suggest that while a relaxed purifying selection is likely to be the dominant force driving accelerated evolution of avian FOXE1 genes, a few residues may have evolved adaptively. This study provides a basis for future genetic and comparative biochemical studies of FOXE1.
authors: Penn Center for Bioinformatics, 1424 Blockley Hall, 423 Guardian Drive, University of Pennsylvania, Philadelphia, PA 19104 USA.
authors: Sergey Yu
authors: SY
authors: Yaklichkin
authors: Diana K
authors: DK
authors: Darnell
authors: Maricela V
authors: MV
authors: Pier
authors: Parker B
authors: PB
authors: Antin
authors: Sridhar
authors: S
authors: Hannenhalli
mesh_terms: D024509:3' Flanking Region / Q000235:genetics; D000818:Animals; D001483:Base Sequence; D002645:Chickens / Q000235:genetics*; D017931:DNA Primers / Q000235:genetics; D019143:Evolution, Molecular; D005241:Feathers / Q000254:growth & development / Q000378:metabolism; D046369:Finches / Q000235:genetics*; D051858:Forkhead Transcription Factors / Q000235:genetics* / Q000378:metabolism; D008969:Molecular Sequence Data; D016133:Polymerase Chain Reaction; D020133:Reverse Transcriptase Polymerase Chain Reaction; D012641:Selection, Genetic; D017422:Sequence Analysis, DNA; D017384:Sequence Deletion; D013961:Thyroid Gland / Q000254:growth & development / Q000378:metabolism; D014422:Turkeys / Q000235:genetics*
chemical_list: D017931:DNA Primers; D051858:Forkhead Transcription Factors