MBE Advance Access published online on February 1, 2007
Molecular Biology and Evolution, doi:10.1093/molbev/msm024
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Research Article |
Functional Divergence in the Arabidopsis ß-1,3-Glucanase Gene Family Inferred by Phylogenetic Reconstruction of Expression States
a Department of Biology, University of Waterloo, Waterloo, Ontario N2L 3G1, Canada
b Current address: Department of Molecular and Cellular Biology, University of Guelph, Guelph, Ontario, N1G 2W1 Canada
Corresponding author: Brendan J. McConkey; E-Mail: mcconkey{at}uwaterloo.ca; Phone: 519-888-4567 x37020; Fax: 519-746-0614
Accepted for publication January 29, 2007.
Plant ß-1,3-glucanases (E.C. 3.2.1.39 [EC] ) comprise large, highly complex gene families involved in pathogen defense as well as a wide range of normal developmental processes. In spite of previous phylogenetic analyses that classify ß-1,3-glucanases by sequence-relatedness, the functional evolution of ß-1,3-glucanases remains unclear. Here, expression and phylogenetic analyses have been integrated in order to investigate patterns of functional divergence in the Arabidopsis ß-1,3-glucanase gene family. Fifty ß-1,3-glucanase genes were grouped into expression classes through clustering of microarray data, and functions were inferred based on knowledge of co-expressed genes and existing literature. The resulting expression classes were mapped as discrete states onto a phylogenetic tree and parsimony reconstruction of ancestral expression states was performed, providing a model of expression divergence. Results showed a highly non-random distribution of developmental expression states in the phylogeny (p = 0.0002) indicating a significant degree of coupling between sequence and developmental expression divergence. A weaker, yet significant level of coupling was found using stress-response data, but not using hormone-response or pathogen-response data. According to the model of developmental expression divergence, the ancestral function was most likely involved in cell division and/or cell wall remodeling. The associated expression state is widely distributed in the phylogeny, is retained by over 25% of gene family members, and is consistent with the known functions of ß-1,3-glucanases in distantly related species and gene families. Consistent with previous hypotheses, pathogenesis-related (PR) ß-1,3-Gs appear to have evolved from ancestral developmentally-regulated ß-1,3-Gs, acquiring PR function through a number of evolutionary events: divergence from the ancestral expression state, acquisition of pathogen/stress-responsive expression patterns, and loss of the C-terminal region including the GPI-anchoring site thus allowing for extracellular secretion.
Key Words: ß-1,3-glucanase • molecular evolution • expression analysis • functional divergence • pathogenesis-related proteins