Abstract
BackgroundMitogen-activated protein kinase (MAPK) cascade is a conserved and universal signal transduction module in organisms. Although it has been well characterized in many plants, no systematic analysis has been conducted in barley.ResultsHere, we identified 20 MAPKs, 6 MAPKKs and 156 MAPKKKs in barley through a genome-wide search against the updated reference genome. Then, phylogenetic relationship, gene structure and conserved protein motifs organization of them were systematically analyzed and results supported the predictions. Gene duplication analysis revealed that segmental and tandem duplication events contributed to the expansion of barley MAPK cascade genes and the duplicated gene pairs were found to undergone strong purifying selection. Expression profiles of them were further investigated in different organs and under diverse abiotic stresses using the available 173 RNA-seq datasets, and then the tissue-specific and stress-responsive candidates were found. Finally, co-expression regulatory network of MAPK cascade genes was constructed by WGCNA tool, resulting in a complicated network composed of a total of 72 branches containing 46 HvMAPK cascade genes and 46 miRNAs.ConclusionThis study provides the targets for further functional study and also contribute to better understand the MAPK cascade regulatory network in barley and beyond.
Highlights
Mitogen-activated protein kinase (MAPK) cascade is a conserved and universal signal transduction module in organisms
Compared to previous study that only 16 HvMAPKs were identified by Krenek et al [28], this study found 20 HvMAPKs, which covered the 16 previous predicted ones, suggesting the whole genome-search could provide more comprehensive prediction of barley MAPK family
20 HvMAPKs, 6 HvMAPKKs and 156 HvMAPKKKs were obtained, which was further supported the existence by Expressed sequence tag (EST) or full-length cDNA sequences
Summary
Mitogen-activated protein kinase (MAPK) cascade is a conserved and universal signal transduction module in organisms It has been well characterized in many plants, no systematic analysis has been conducted in barley. Extensive studies have revealed that the MAPK cascades widely involved in regulating many biological processes, including cell division, plant development, growth and hormonal response as well as in response to diverse biotic and abiotic stresses, such as drought, salt, heat and pathogen infection [5,6,7] In light of their importance, a large number of MAPK genes have been functionally identified in several plants, including Arabidopsis [8], rice [9,10,11], Brachypdoium [12, 13] and maize [14, 15]. The recently published reference-quality barley genome [26] makes it possible to conduct a comprehensive identification of its MAPK cascade gene families at whole genome scale and construct the MAPK signal transduction pathway
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