English (United Kingdom)

https://curated-unify.zendy.io/wp-json/zendy-region/v1/featured_content/oa?rat=en

https://curated-unify.zendy.io/wp-json/zendy-region/v1/highlighted_journal/

Global: Zendy Plus annual

Presents the access of premium content as premium feature

Premium Content

Presents the keyphrase highlighting as premium feature

Keyphrase Highlighting

Presents the summarisation as premium feature

Summarisation

Insights

Presents the pdf analysis as premium feature

PDF Analysis

Presents the zaia usage as premium feature

ZAIA

Global: Zendy Tools annual

Global: Zendy Free Plan

Global: Zendy Tools monthly

Global: Zendy Plus monthly

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.    Electronic supplementary material  The online version of this article (doi:10.1186/1471-2164-15-548) contains supplementary material, which is available to authorized users.

The Arabidopsis Kinome: phylogeny and evolutionary insights into functional diversification