Abstract
BackgroundMembers 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.MethodsMEKKs 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.ResultsWith 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.ConclusionsExpansion 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.Electronic supplementary materialThe online version of this article (doi:10.1186/s12864-015-2228-3) contains supplementary material, which is available to authorized users.
Highlights
Members of the plant MAP Kinases superfamily have been mostly studied in Arabidopsis thaliana and little is known in most other species
Apart from the already known Fertilizationrelated kinase (FRK), ScFRK1, 2 and 3 [44, 45], three new FRK members were found in the combined ovule/pollen transcriptome and named ScFRK4, 5 and 6
The family can be further divided in three groups: 1) one including ScFRK1, 2 and 6 with no Arabidopsis ortholog; 2) one including ScFRK3, 4 and AtMAPKKK19, 20 and 21; 3) and a third group represented by ScFRK5 alone
Summary
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. A. thaliana contains 10 MAPKKKKs, around 80 MAPKKKs (divided into three subfamilies, the MEKKs, the RAFs and the ZIKs) [8], 10 MAPKKs and 20 MAPKs [3, 9], only few complete cascades have been deciphered These include the MEKK1 - MKK4/5 – MPK3/6 cascade that positively regulates plant innate immunity [10] and acts in phytoalexin biosynthesis [11]. It was shown that the zygote could not divide properly, leading to inappropriate cell divisions of the suspensor and, eventually, to the development of an embryo without the root primordium [20]
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