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MBE Advance Access published online on August 18, 2004
Molecular Biology and Evolution, doi:10.1093/molbev/msh235
Molecular Biology and Evolution © Society for Molecular Biology and Evolution 2004; all rights reserved
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Accepted August 10, 2004

Original Article

The Evolutionary Implications of knox-I Gene Duplications in Conifers: Correlated Evidence from Phylogeny, Gene Mapping, and Analysis of Functional Divergence

Carine Guillet-Claude 1, Nathalie Isabel 2, Betty Pelgas 1, Jean Bousquet 1*

1 Arborea and Chaire de recherche du Canada en génomique forestière et environnementale, Centre de recherche en biologie forestière, Université Laval, Sainte-Foy, Québec G1K 7P4 Canada
2 Arborea and Chaire de recherche du Canada en génomique forestière et environnementale, Centre de recherche en biologie forestière, Université Laval, Sainte-Foy, Québec G1K 7P4 Canada; Natural Resources Canada, Canadian Forest Service, Laurentian Forestry Centre, Sainte-Foy, Québec G1V 4C7 Canada

* To whom correspondence should be addressed. E-mail: bousquet{at}rsvs.ulaval.ca.


  Abstract

Class I knox genes code for transcription factors that play an essential role in plant growth and development as central regulators of meristem cell identity. Based on the analysis of new cDNA sequences from various tissues and genomic DNA sequences, we identified a highly diversified group of class I knox genes in conifers. Phylogenetic analyses of complete amino acid sequences from various seed plants indicated that all conifer sequences formed a monophyletic group. Within conifers, four subgroups here named genes KN1 to KN4 were well delineated, each regrouping pine and spruce sequences. KN4 was sister group to KN3, which was sister group to KN1 and KN2. Genetic mapping on the genomes of two divergent Picea species indicated that KN1 and KN2 are located close to each other on the same linkage group, while KN3 and KN4 mapped on different linkage groups, correlating the more ancient divergence of these two genes. The proportion of synonymous and nonsynonymous substitutions suggested intense purifying selection for the four genes. However, rates of substitution per year indicated an evolution in two steps: faster rates were noted after gene duplications, followed subsequently by lower rates. Positive directional selection was detected for most of the internal branches harbouring an accelerated rate of evolution. In addition, many sites with highly significant amino acid rate shift were identified between these branches. However, the tightly linked KN1 and KN2 did not diverge as much from each other. The implications of the correlation between phylogenetic, structural, and functional information are discussed in relation to the diversification of the knox-I gene family in conifers.

Keywords: conifer knox-I genes; evolutionary rates; functional divergence; gene duplication; genome mapping; phylogenetic analysis.
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