Abstract
BackgroundIn plants, tandem, segmental and whole-genome duplications are prevalent, resulting in large numbers of duplicate loci. Recent studies suggest that duplicate genes diverge predominantly through the partitioning of expression and that breadth of gene expression is related to the rate of gene duplication and protein sequence evolution.Here, we utilize expressed sequence tag (EST) data to study gene duplication and expression patterns in the monosaccharide transporter (MST) gene family across the land plants. In Arabidopsis, there are 53 MST genes that form seven distinct subfamilies. We created profile hidden Markov models of each subfamily and searched EST databases representing diverse land plant lineages to address the following questions: 1) Are homologs of each Arabidopsis subfamily present in the earliest land plants? 2) Do expression patterns among subfamilies and individual genes within subfamilies differ across lineages? 3) Has gene duplication within each lineage resulted in lineage-specific expansion patterns? We also looked for correlations between relative EST database representation in Arabidopsis and similarity to orthologs in early lineages.ResultsHomologs of all seven MST subfamilies were present in land plants at least 400 million years ago. Subfamily expression levels vary across lineages with greater relative expression of the STP, ERD6-like, INT and PLT subfamilies in the vascular plants. In the large EST databases of the moss, gymnosperm, monocot and eudicot lineages, EST contig construction reveals that MST subfamilies have experienced lineage-specific expansions. Large subfamily expansions appear to be due to multiple gene duplications arising from single ancestral genes. In Arabidopsis, one or a few genes within most subfamilies have much higher EST database representation than others. Most highly represented (broadly expressed) genes in Arabidopsis have best match orthologs in early divergent lineages.ConclusionThe seven subfamilies of the Arabidopsis MST gene family are ancient in land plants and show differential subfamily expression and lineage-specific subfamily expansions. Patterns of gene expression in Arabidopsis and correlation of highly represented genes with best match homologs in early lineages suggests that broadly expressed genes are often highly conserved, and that most genes have more limited expression.
Highlights
In plants, tandem, segmental and whole-genome duplications are prevalent, resulting in large numbers of duplicate loci
The seven subfamilies of the Arabidopsis monosaccharide transporter (MST) gene family are ancient in land plants and show differential subfamily expression and lineage-specific subfamily expansions
Phylogenetic analysis and mapping of the MST gene family in Arabidopsis Phylogenetic analysis of the 53 Arabidopsis MST protein sequences using the maximum likelihood (ML) method (Figure 1) revealed a phylogeny in agreement with the phylogeny posted on the Arabidopsis Sugar Transporter homepage [23], with one notable exception: In our ML tree, the AtSTP13 protein clusters at the base of the subclade containing the AtSTP2, -6 and -8 genes, rather than grouping with the AtSTP14 and AtSTP7 genes
Summary
Tandem, segmental and whole-genome duplications are prevalent, resulting in large numbers of duplicate loci. We utilize expressed sequence tag (EST) data to study gene duplication and expression patterns in the monosaccharide transporter (MST) gene family across the land plants. Gene families appear to evolve through a combination of tandem, segmental and whole genome duplication (polyploidy) events. The classical model of the fates of duplicate genes [2,3,4] predicts that most gene duplicates are lost due to deleterious mutations and that new function arises only with rare beneficial mutations resulting from neutral processes. More recent theoretical and empirical work suggests that gene duplicates are retained more frequently than the classical model permits and that new function or expression arises through the processes of neo- and subfunctionalization [5,6]. Many gene duplicate pairs appear to evolve slowly, suggesting that buffering of crucial functions may be important after gene duplication events [10]
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