title: Genome-wide analysis of MAPKKKs shows expansion and evolution of a new MEKK class involved in solanaceous species sexual reproduction.
abstract: BACKGROUND
  Members of the plant MAP Kinases superfamily have been mostly studied in Arabidopsis thaliana and little is known in most other species. In Solanum chacoense, a wild species close to the common potato, it had been reported that members of a specific group in the MEKK subfamily, namely ScFRK1 and ScFRK2, are involved in male and female reproductive development. Apart from these two kinases, almost nothing is known about the roles of this peculiar family.
  
  
  METHODS
  MEKKs were identified using BLAST and hidden Markov model (HMM) to build profiles using the 21 MEKKs from A. thaliana. Following protein sequence alignments, the neighbor-joining method was used to reconstruct phylogenetic trees of the MEKK subfamily. Kinase subdomains sequence logos were generated with WebLogo in order to pinpoint FRK distinct motifs. Codon alignments of the FRKs kinase subdomains and maximum-likelihood phylogenetic trees were used in the codon substitution models of the codeml program in the PAML package to detect selective pressure between FRK groups.
  
  
  RESULTS
  With the recent progress in Next-Generation Sequencing technologies, the genomes and transcriptomes of numerous plant species have been recently sequenced, giving access to a vast amount of data. With the aim of finding all members of the MEKK subfamily members in plants, we screened the genomes of 15 species from different clades of the plant kingdom. Interestingly, the whole MEKK subfamily has significantly expanded throughout evolution, especially in solanaceous species. This holds true for members of the FRK class, which have also strongly expanded and diverged.
  
  
  CONCLUSIONS
  Expansion and rapid evolution of the FRK class members in solanaceous species support the hypothesis that they have acquired new roles, mainly in male and female reproductive development.
authors.affiliation: Institut de Recherche en Biologie Végétale, Département de Sciences Biologiques, Université de Montréal, 4101 rue Sherbrooke est, Montréal, H1X 2B2, QC, Canada. caroline.daigle@umontreal.ca.
authors.forename: Caroline
authors.initials: C
authors.lastname: Daigle
authors.affiliation: Institut de Recherche en Biologie Végétale, Département de Sciences Biologiques, Université de Montréal, 4101 rue Sherbrooke est, Montréal, H1X 2B2, QC, Canada. dp.matton@umontreal.ca.
authors.forename: Daniel P
authors.initials: DP
authors.lastname: Matton
mesh_terms: D019295:Computational Biology / Q000379:methods; D017124:Conserved Sequence; D019143:Evolution, Molecular; D020869:Gene Expression Profiling; D018506:Gene Expression Regulation, Plant; D017343:Genes, Plant; D018745:Genome, Plant; D055106:Genome-Wide Association Study; D059014:High-Throughput Nucleotide Sequencing; D020930:MAP Kinase Kinase Kinases / Q000235:genetics* / Q000378:metabolism; D005810:Multigene Family; D059372:Nucleotide Motifs; D010802:Phylogeny; D012098:Reproduction / Q000235:genetics*; D032322:Solanum / Q000235:genetics* / Q000378:metabolism; D059467:Transcriptome
chemical_list: D020930:MAP Kinase Kinase Kinases