| Post-translational modifications(PTMs)including phosphorylation,ubiquitination,methylation,acetylation,and glycosylation greatly increase protein complexity and dynamics.These modifications lead to the changes of protein structural,and regulate the activity,stability,subcellular localization,and interactions with other proteins.Thus,they are raising as key mechanisms in the regulation of various biological events.Protein phosphorylation,catalyzed by protein kinases(PKs),is one of the most important and well investgated PTMs.PKs constitute one of the largest gene families in eukaryotic genomes.They are involved in numerous cellular and biological processes,such as cell expansion,seed germination,plant development,pollen tube growth,response to various abiotic and biotic stresses and so on.However,relative to the model plants including Arabidopsis,rice,and maize,functional investgations of PKs in horticultural plants are quite limited yet.Grape(Vitis vinifera)is one of the most popular and economically important fruits around the world.Grape production,similar to that of other crops,however,must address abiotic and biotic stresses,which cause reductions in yield and fruit quality.Pineapple(Ananas comosus)is an important tropical fruit possessing crassulacean acid metabolism(CAM),a photosynthetic carbon assimilation pathway with high water-use efficiency.The CAM plants use just one-sixth water consumed by C3 plants.Comparative analysis of the kinome between grapevine and pineapple helped us to understand the differences of the PK families between C3 and CAM plants.In this study,we systematically indentified all the PKs from grapevine and pineapple,analyzed their expansion mechanisms,selection modes,gene expression patterns,and coexpression networks.The main results are as follows:1.1168 PK-encoding genes were totally identified in grape genome,and classified into 20 groups and 121 families,with the RLK group being the largest group,containing 872 members.The 1168 PK genes were randomly distributed on all 19 chromosomes.395 and 231 PK genes generated from tandem duplication and segmental duplication,respectively,indicating both tandem and segmental duplications contributed to the expansion of the grapevine kinome,especially the expansion of RLK group.Ka/Ks values of duplication events indicated that most of the tandemly and segmentally duplicated genes were under purifying selection.We further demonstrated that the grapevine kinome families exhibited different expression patterns during development and in response to various treatments,with many being coexpressed.The results of RNA-Seq and qRT-PCR helped us to identified four candidate genes which response to both drought and NaCl stresses.2.High-throughput transcriptome sequencing of grapevine seedings subjected to drought stress for 0(control),2,4 and 8 days were presented.A total of 1482 genes were identified as differentially expressed genes(DEGs),619 of which were up-regulated,and 863 were down-regulated under drought stress.Gene ontology(GO)enrichment analyses showed that the up-regulated DEGs were all enriched in biological process and molecular function.KEGG pathway enrichment results performed that part DEGs in different time points enriched in plant hormone signal transduction pathway,indicating that hormones were required for plant drought response.Among the 1482 DEGs,we further found 65 PK genes,which might play key roles in grapevine response to drought stress,most of them were RLK and CAMK group members.Our transcriptome analyse provided a valuable resource for grapevine breeding and investigation in grapevine response to drought stress,candidate genes can be used to guide future researches to breed drought tolerant grapevine cultivars.3.In this study,a total of 758 predicted PK genes were systematically identified in pineapple genome.We further classified the pineapple kinome into 20 groups and 116 families based on the kinase domain sequences.The subcellular location prediction results of pineapple PKs reveled that more than 50%of RLK members localized to the plasma membrane.Both segmental and tandem duplication contributed greatly to the expansion of pineapple kinome based on the collinearity analysis,especially the expansion of RLK group.Ka/Ks ratios showed that almost all of the tandem and segmental duplication events were under purifying selection.Previous studies reported that the circadian rhythms of genes in CAM plants played critical roles.The RNA-Seq analysis revealed that pineapple PKs exhibit different tissue-specific and diurnal rhythm expression patterns.Forty PK genes performed higher expression levels in green leaf tip than in white leaf base,and fourteen of them had strong differential expression patterns between the photosynthetic green leaf tip and the non-photosynthetic white leaf base,only being up-regulated in the green tip tissue.Gene duplications,expression patterns,and coexpression networks helped us to quickly identify the key candidate genes in pineapple kinome,which may function in the CO2 fixation process in pineapple,and help engineering CAM pathway into C3 crops to improve drought tolerance.These findings provide insights into the evolution and molecular functions of pineapple PKs,and lay a foundation for further functional analysis of PKs in CAM plants.4.We further compared the classification results of kinase superfamilies between two fruit crops,grapevine and pineapple.1168 and 758 PK genes were identified in grapevine and pineapple genome,respectively.RLKs comprised a major group in plant kinome,with 480 encoded in the pineapple genome and 872 in grapevine genome.The greater number of RLKs in grapevine was mostly attributable to the tandem duplication events.We further analyzed the classification results of kinomes from 25 plant species,and found that two CAM plant(pineapple and kalanchoe)kinomes were smaller than most C3 plant kinomes in seed plants.Our results provide a valuable insight into comparative analysis of the kinomes between C3 and CAM plants,and need to be confirmed by analyzing more plant kinomes. |
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