DOI: 10.5061/dryad.pq7d7
title: Data from: The Arabidopsis kinome: phylogeny and evolutionary insights into functional diversification

description: 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.
description: Phylogeny of Arabidopsis
 eukaryotic kinasesPhylogeny of 942
 eukaryotic kinase domains of Arabidopsis proteins. An alignment of 491
 eukaryotic protein kinases was downloaded on Feb 9, 2012 from
 http://kinase.com/human/kinome/phylogeny.html, and this alignment was used
 to compute a profile Hidden Markov Model (HMM) using the software HMMer
 [12]. All representative gene models from Arabidopsis thaliana
 (TAIR10_pep) were searched against the profile HMM using HMMer. In total,
 1,045 sequences generated hits with an E-value lower than 0.01. These
 sequences were then aligned to the profile HMM. Two sequences (AT1G11300.1
 and AT2G32800.1) each had two distinct kinase domains and both domains per
 gene were therefore included as separate sequences in the alignment,
 resulting in an alignment of 1,047 distinct Arabidopsis kinase domains
 (additional File 5). All alignment positions not part of the profile HMM
 were removed from the alignment. In addition, all sequences covering less
 than 70% of the profileHMM were removed using the software REAP [13]. The
 cutoff value of 70% corresponded to a threshold value in sequence coverage
 distribution with sharp decline of sequence coverage for 111 kinase
 domains below coverage of 70% (additional File 8). The final alignment
 then consisted of 317 columns from 942 sequences (kinase domains) and was
 used to compute a maximum likelihood phylogeny and 100 bootstrap
 replicates using the PROTCATWAG model of the RAxML program
 [14].TREE_familie
 groups_20.02.2012