The wild strawberry kinome: identification, classification and transcript profiling of protein kinases during developmen
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RESEARCH ARTICLE
Open Access
The wild strawberry kinome: identification, classification and transcript profiling of protein kinases during development and in response to gray mold infection Hui Liu1, Wei Qu1, Kaikai Zhu2 and Zong-Ming ( Max) Cheng1,3*
Abstract Background: Protein kinases (PKs) play an important role in signaling cascades and are one of the largest and most conserved protein super families in plants. Despite their importance, the woodland strawberry (Fragaria vesca) kinome and expression patterns of PK genes remain to be characterized. Results: Here, we report on the identification and classification of 954 Fragaria vesca PK genes, which were classified into nine groups and 124 gene families. These genes were distributed unevenly among the seven chromosomes, and the number of introns per gene varied from 0 to 47. Almost half of the putative PKs were predicted to localize to the nucleus and 24.6% were predicted to localize to the cell membrane. The expansion of the woodland strawberry PK gene family occurred via different duplication mechanisms and tandem duplicates occurred relatively late as compared to other duplication types. Moreover, we found that tandem and transposed duplicated PK gene pairs had undergone stronger diversifying selection and evolved relatively faster than WGD genes. The GO enrichment and transcriptome analysis implicates the involvement of strawberry PK genes in multiple biological processes and molecular functions in differential tissues, especially in pollens. Finally, 109 PKs, mostly the receptor-like kinases (RLKs), were found transcriptionally responsive to Botrytis cinerea infection. Conclusions: The findings of this research expand the understanding of the evolutionary dynamics of PK genes in plant species and provide a potential link between cell signaling pathways and pathogen attack. Keywords: Strawberry protein kinases, Gene duplication, Receptor-like kinases (RLKs), Transcript profiling, Botrytis cinerea infection
Background Protein kinases (PK) are a large and widely distributed protein superfamily found in prokaryotes and eukaryotes and comprise one of the largest and most conserved protein gene super-families in plants. They play important roles in various signaling pathways via phosphorylation of serine, * Correspondence: [email protected]; [email protected] 1 College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China 3 Department of Plant Sciences, University of Tennessee, Knoxville 37996, USA Full list of author information is available at the end of the article
threonine, and tyrosine amino acids in target proteins. The first plant protein kinases to be identified and characterized were from Pisum sativum in 1973 [1]. In Arabidopsis thaliana, there are more than 1000 PKs, collectively called a kinome [2], and many PKs in other plant species have been reported, including soybean [3], tobacco [4], cotton [5] and rice [6]. In general, PK gene families are bigger in plant genomes than in those of animals [7, 8]. For example, in humans, PKs o
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