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Previous studies of gene diversity in the homeobox superclass have shown that the Florida amphioxus Branchiostoma floridae has undergone remarkably little gene family loss. Here we use a combined BLAST and HMM search strategy to assess the family level diversity of four other transcription factor superclasses: the Paired/Pax genes, Tbx genes, Fox genes and Sox genes. We apply this across genomes from five chordate taxa, including B. floridae and Ciona intestinalis, plus two outgroup taxa. Our results show scattered gene family loss. However, as also found for homeobox genes, B. floridae has retained all ancient Pax, Tbx, Fox and Sox gene families that were present in the common ancestor of living chordates. We conclude that, at least in terms of transcription factor gene complexity, the genome of amphioxus has experienced remarkable stasis compared to the genomes of other chordates.

Original publication

DOI

10.1093/bfgp/els012

Type

Journal article

Journal

Brief Funct Genomics

Publication Date

03/2012

Volume

11

Pages

177 - 186

Keywords

Animals, Biological Evolution, Chordata, Genetic Variation, Genome, Homeodomain Proteins, Transcription Factors