Data from: The Arabidopsis kinome: phylogeny and evolutionary insights into functional diversification

Background: Protein kinases constitute a particularly large protein family
in Arabidopsis with important functions in cellular signal transduction
networks. At the same time Arabidopsis is a model plant with high
frequencies of gene duplications. Here, we have conducted a systematic
analysis of the Arabidopsis kinase complement, the kinome, with particular
focus on gene duplication events. We matched Arabidopsis proteins to a
Hidden-Markov Model of eukaryotic kinases and computed a phylogeny of 942
Arabidopsis protein kinase domains and mapped their origin by gene
duplication. Results: The phylogeny showed two major clades of receptor
kinases and soluble kinases, each of which was divided into functional
subclades. Based on this phylogeny, association of yet uncharacterized
kinases to families was possible which extended functional annotation of
unknowns. Classification of gene duplications within these protein kinases
revealed that representatives of cytosolic subfamilies showed a tendency
to maintain segmentally duplicated genes, while some subfamilies of the
receptor kinases were enriched for tandem duplicates. Although functional
diversification is observed throughout most subfamilies, some instances of
functional conservation among genes transposed from the same ancestor were
observed. In general, a significant enrichment of essential genes was
found among genes encoding for protein kinases. Conclusions: The inferred
phylogeny allowed classification and annotation of yet uncharacterized
kinases. The prediction and analysis of syntenic blocks and duplication
events within gene families of interest can be used to link functional
biology to insights from an evolutionary viewpoint. The approach
undertaken here can be applied to any gene family in any organism with an
annotated genome.