Plant Molecular Biology

, Volume 72, Issue 3, pp 247–263 | Cite as

Genome-wide analysis of the chalcone synthase superfamily genes of Physcomitrella patens

  • P. K. Harshavardhan Koduri
  • Graeme S. Gordon
  • Elizabeth I. Barker
  • Che C. Colpitts
  • Neil W. Ashton
  • Dae-Yeon Suh


Enzymes of the chalcone synthase (CHS) superfamily catalyze the production of a variety of secondary metabolites in bacteria, fungi and plants. Some of these metabolites have played important roles during the early evolution of land plants by providing protection from various environmental assaults including UV irradiation. The genome of the moss, Physcomitrella patens, contains at least 17 putative CHS superfamily genes. Three of these genes (PpCHS2b, PpCHS3 and PpCHS5) exist in multiple copies and all have corresponding ESTs. PpCHS11 and probably also PpCHS9 encode non-CHS enzymes, while PpCHS10 appears to be an ortholog of plant genes encoding anther-specific CHS-like enzymes. It was inferred from the genomic locations of genes comprising it that the moss CHS superfamily expanded through tandem and segmental duplication events. Inferred exon–intron architectures and results from phylogenetic analysis of representative CHS superfamily genes of P. patens and other plants showed that intron gain and loss occurred several times during evolution of this gene superfamily. A high proportion of P. patens CHS genes (7 of 14 genes for which the full sequence is known and probably 3 additional genes) are intronless, prompting speculation that CHS gene duplication via retrotransposition has occurred at least twice in the moss lineage. Analyses of sequence similarities, catalytic motifs and EST data indicated that a surprisingly large number (as many as 13) of the moss CHS superfamily genes probably encode active CHS. EST distribution data and different light responsiveness observed with selected genes provide evidence for their differential regulation. Observed diversity within the moss CHS superfamily and amenability to gene manipulation make Physcomitrella a highly suitable model system for studying expansion and functional diversification of the plant CHS superfamily of genes.


Physcomitrella patens Chalcone synthase superfamily Multigene family Enzyme evolution Gene duplication Retrotransposition Gene regulation cis-acting elements 



This research was supported by the Natural Sciences and Engineering Research Council of Canada (NSERC) and the University of Regina. E. I. B. and C. C. C. are recipients of NSERC postgraduate scholarships (PGS-D and CGS-M, respectively).

Supplementary material

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Supplementary material 1 (DOC 91 kb)


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Copyright information

© Springer Science+Business Media B.V. 2009

Authors and Affiliations

  • P. K. Harshavardhan Koduri
    • 1
  • Graeme S. Gordon
    • 1
  • Elizabeth I. Barker
    • 2
  • Che C. Colpitts
    • 1
  • Neil W. Ashton
    • 2
  • Dae-Yeon Suh
    • 1
  1. 1.Department of Chemistry and BiochemistryUniversity of ReginaReginaCanada
  2. 2.Department of BiologyUniversity of ReginaReginaCanada

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