Genome-wide identification of MAPK, MAPKK, and MAPKKK gene families and transcriptional profiling analysis during development and stress response in cucumber

Abstract

BackgroundThe mitogen-activated protein kinase (MAPK) cascade consists of three types of reversibly phosphorylated kinases, namely, MAPK, MAPK kinase (MAPKK/MEK), and MAPK kinase kinase (MAPKKK/MEKK), playing important roles in plant growth, development, and defense response. The MAPK cascade genes have been investigated in detail in model plants, including Arabidopsis, rice, and tomato, but poorly characterized in cucumber (Cucumis sativus L.), a major popular vegetable in Cucurbitaceae crops, which is highly susceptible to environmental stress and pathogen attack.ResultsA genome-wide analysis revealed the presence of at least 14 MAPKs, 6 MAPKKs, and 59 MAPKKKs in the cucumber genome. Phylogenetic analyses classified all the CsMAPK and CsMAPKK genes into four groups, whereas the CsMAPKKK genes were grouped into the MEKK, RAF, and ZIK subfamilies. The expansion of these three gene families was mainly contributed by segmental duplication events. Furthermore, the ratios of non-synonymous substitution rates (Ka) and synonymous substitution rates (Ks) implied that the duplicated gene pairs had experienced strong purifying selection. Real-time PCR analysis demonstrated that some MAPK, MAPKK and MAPKKK genes are preferentially expressed in specific organs or tissues. Moreover, the expression levels of most of these genes significantly changed under heat, cold, drought, and Pseudoperonospora cubensis treatments. Exposure to abscisic acid and jasmonic acid markedly affected the expression levels of these genes, thereby implying that they may play important roles in the plant hormone network.ConclusionA comprehensive genome-wide analysis of gene structure, chromosomal distribution, and evolutionary relationship of MAPK cascade genes in cucumber are present here. Further expression analysis revealed that these genes were involved in important signaling pathways for biotic and abiotic stress responses in cucumber, as well as the response to plant hormones. Our first systematic description of the MAPK, MAPKK, and MAPKKK families in cucumber will help to elucidate their biological roles in plant.Electronic supplementary materialThe online version of this article (doi:10.1186/s12864-015-1621-2) contains supplementary material, which is available to authorized users.

Genome-Wide Identification and Expression Analysis of the Mitogen-Activated Protein Kinase Gene Family in Cassava

“…As shown in Figure 1, 21 MeMAPKs were classified into four different groups (groups A, B, C, and D) together with their MAPK orthologs in various species, which is in accordance with previous phylogenetic classifications of MAPKs (Ichimura et al, 2002; Wang et al, 2015). Group A contained 3 genes, group B contained 7 genes, and group C contained 2 genes, while group D was the largest clade with 9 MeMAPK genes.…”

High-throughput gene-expression quantification of grapevine defense responses in the field using microfluidic dynamic arrays

“…The induced immunity activates a wide variety of defense mechanisms that involve passive defense mechanisms [4] that restrict the entry or spread of the pathogen in the plant, but also active defense mechanisms that prevent the development of the pathogen by confining it to the site of infection or causing its death. The most common early cellular responses are mechanisms of ion flux changes, production of reactive oxygen species (ROS) and phosphorylation mechanisms/dephosphorylation (mitogen -activated protein kinase or MAPKKK, MAPKK and MAPK [5–7]. After these early steps, some secondary metabolic pathways are stimulated and allow the generalization of the response to the whole plant, while systemic acquired resistance (SAR) is being established [8, 9].…”

Genome-wide identification of MAPKKK genes and their responses to phytoplasma infection in Chinese jujube (Ziziphus jujuba Mill.)

“…In addition, the alignments of all Arabidopsis MAPKKK sequences were used to construct an HMM profile (http://hmmer.org/download.html) to search for other potential MAPKKK members in the jujube genome database. All the potential ZjMAPKKK genes that contain a protein kinase domain (PF00069) were confirmed by HMMER tools [35], redundancy was removed, and the remaining sequences were identified as belonging to the ZjMAPKKK family. Furthermore, the ExPASy Proteomics Server (http://expasy.org/) was used to calculate the theoretical pI (isoelectric point) and Mw (molecular weight) of the putative ZjMAPKKKs [36].…”