A genome-wide view of transcription factor gene diversity in chordate evolution: Less gene loss in amphioxus?

Jordi Paps, Peter W.H. Holland, Sebastian M. Shimeld*

*Corresponding author for this work

Research output: Contribution to journalArticle (Academic Journal)

28 Citations (Scopus)

Abstract

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 languageEnglish
Article numberels012
Pages (from-to)177-186
Number of pages10
JournalBriefings in Functional Genomics
Volume11
Issue number2
DOIs
Publication statusPublished - 1 Mar 2012

Keywords

  • Fox
  • Homeobox
  • Pax
  • Sox
  • T-box

Fingerprint Dive into the research topics of 'A genome-wide view of transcription factor gene diversity in chordate evolution: Less gene loss in amphioxus?'. Together they form a unique fingerprint.

  • Cite this