The Evolution of Alternative Splicing in the Pax Family: The View from the Basal Chordate Amphioxus

  • Stephen Short
  • Linda Z. Holland


Pax genes encode transcription factors critical for metazoan development. Large-scale gene duplication with subsequent gene losses during vertebrate evolution has resulted in two human genes for each of the Pax1/9, Pax3/7, and Pax4/6 subfamilies and three for the Pax2/5/8 subfamily, compared to one each in the cephalochordate amphioxus. In addition, alternative splicing occurs in vertebrate Pax transcripts from all four subfamilies, and many splice forms are known to have functional importance. To better understand the evolution of alternative splicing within the Pax family, we systematically surveyed transcripts of the four amphioxus Pax genes. We have found alternative splicing in every gene. Comparisons with vertebrates suggest that the number of alternative splicing events per gene has not decreased following duplication; there are comparable levels in the four amphioxus Pax genes as in each gene of the equivalent vertebrate families. Thus, the total number of isoforms for the nine vertebrate genes is considerably higher than for the four amphioxus genes. Most alternative splicing events appear to have arisen since the divergence of amphioxus and vertebrate lineages, suggesting that differences in alternative splicing could account for divergent functions of the highly conserved Pax genes in both lineages. However, several events predicted to dramatically alter known functional domains are conserved between amphioxus and vertebrates, suggestive of a common chordate function. Our results, together with previous studies of vertebrate Pax genes, support the theory that alternative splicing impacts functional motifs more than gene duplication followed by divergence.


Pax Alternative splicing Amphioxus Branchiostoma Gene duplication 



We would like to thank John Lawrence for his hospitality at the University of South Florida. We also thank Zbynek Kozmik, Christine Beardsley, and Colin Sharpe for helpful criticism and comments on the manuscript. This work was supported by Grant MCB06-20019 from the National Science Foundation to L.Z.H.

Supplementary material

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© Springer Science+Business Media, LLC 2008

Authors and Affiliations

  1. 1.Marine Biology Research DivisionScripps Institution of OceanographyLa JollaUSA

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