Abstract
WRKY transcription factors belong to one of the largest transcription factor families. These factors possess functions in plant growth and development, signal transduction, and stress response. Here, we identified 95 DcWRKY genes in carrot based on the carrot genomic and transcriptomic data, and divided them into three groups. Phylogenetic analysis of WRKY proteins from carrot and Arabidopsis divided these proteins into seven subgroups. To elucidate the evolution and distribution of WRKY transcription factors in different species, we constructed a schematic of the phylogenetic tree and compared the WRKY family factors among 22 species, which including plants, slime mold and protozoan. An in-depth study was performed to clarify the homologous factor groups of nine divergent taxa in lower and higher plants. Based on the orthologous factors between carrot and Arabidopsis, 38 DcWRKY proteins were calculated to interact with other proteins in the carrot genome. Yeast two-hybrid assay showed that DcWRKY20 can interact with DcMAPK1 and DcMAPK4. The expression patterns of the selected DcWRKY genes based on transcriptome data and qRT-PCR suggested that those selected DcWRKY genes are involved in root development, biotic and abiotic stress response. This comprehensive analysis provides a basis for investigating the evolution and function of WRKY genes.
Highlights
Transcriptional regulation is the most important link for regulating gene expression in plants
To identify all the WRKY factors in the carrot genome, we employed the HMM profile of the WRKY domain (PF03106) as a query to search against the database using HMMER3.0 and BLAST
Seventeen genes were identified to group I, which contained two WRKY domains and had a zinc finger motif of C2H2 type (C-X4-C-X22–23-H-X1-H)
Summary
Transcriptional regulation is the most important link for regulating gene expression in plants. Group III contains only one domain but has a C2HC zinc finger type (C-X7-C-X23-H-X1-C)[6] Wu and his colleagues further analyzed the WRKY family in Arabidopsis and rice and revealed the distribution of group II into three subgroups (IIa+ b, IIc, and IId+ e) based on sequence similarities[9]. A large number of WRKY factors were found, but the functions of only a small number of these factors have been analyzed further These WRKY factors are involved in seed germination, plant growth and development, signal transduction, and metabolic regulation[18,19,20]. They participate in biotic and abiotic stress responses, such as freezing, salinity, drought, and pathogen infection[21,22]. MiR396 regulates HaWRKY6 in response to high-temperature damage[27]
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