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 Received: 5 July 2009 / Accepted: 19 October 2009 / Published online: 31 October 2009 Ó Springer Science+Business Media B.V. 2009 Abstract Enzymes of the chalcone synthase (CHS) superfamily catalyze the production of a variety of sec- ondary 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 infer- red from the genomic locations of genes comprising it that the moss CHS superfamily expanded through tandem and segmental duplication events. Inferred exon–intron archi- tectures and results from phylogenetic analysis of repre- sentative 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 similari- ties, catalytic motifs and EST data indicated that a sur- prisingly large number (as many as 13) of the moss CHS superfamily genes probably encode active CHS. EST dis- tribution 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. Keywords Physcomitrella patens Á Chalcone synthase superfamily Á Multigene family Á Enzyme evolution Á Gene duplication Á Retrotransposition Á Gene regulation Á cis-acting elements Introduction Chalcone synthase (CHS, E.C. 2.3.1.74) catalyzes the first committed step of flavonoid biosynthesis. CHS condenses a phenylpropanoid CoA ester (e.g., p-coumaroyl-CoA) with three acetate units from malonyl-CoA molecules, and cyclizes the resulting intermediate to produce a chalcone (e.g., naringenin chalcone), the precursor of diverse flavonoids (Fig. 1a). CHS is the representative member of the CHS superfamily, also known as type III polyketide synthases, and is found in all plant species. Enzymes of the CHS superfamily exhibit similarity in sequence, structure and general catalytic principles in that they are homodi- mers of 40–45 kDa subunits and all contain a Cys-His-Asn catalytic triad in the active site (Fig. 1b, c; Schro ¨der 1997; Electronic supplementary material The online version of this article (doi:10.1007/s11103-009-9565-z) contains supplementary material, which is available to authorized users. P. K. H. Koduri Á G. S. Gordon Á C. C. Colpitts Á D.-Y. Suh (&) Department of Chemistry and Biochemistry, University of Regina, 3737 Wascana Parkway, Regina, SK S4S 0A2, Canada e-mail: suhdaey@uregina.ca E. I. Barker Á N. W. Ashton Department of Biology, University of Regina, 3737 Wascana Parkway, Regina, SK S4S 0A2, Canada 123 Plant Mol Biol (2010) 72:247–263 DOI 10.1007/s11103-009-9565-z