Genome-Wide Analysis of WRKY Genes and Their Response to Hormone and Mechanic Stresses in Carrot

This study provides an in-depth insight into the evolution and expression of WRKY gene family in carrot. Materials and Methods Identification of Putative WRKY Proteins in Carrot To comprehensively identify the carrot WRKY genes, genome sequences of this plant were downloaded from the Phytozome (https://phytozome.jgi.doe.gov/pz/portal.html#) (Iorizzo et al., 2016), and the WRKY domain (PF03106) was downloaded from Pfam (http://pfam.xfam.org/). All candidate carrot WRKY genes were firstly obtained via searching against the genome with PF03106 file using HMMER3.0 software (http://hmmer.janelia.org/) with parameters as “-E 1e-10 -domE 1e-10.” Then, the conserved domain peptides of the initially identified WRKY members were aligned with MUSCLE (Edgar, 2004) to build carrot-specific HMM file for the WRKY family, and the file was used for the next HMM searches. Finally, the sequences were confirmed using SMART database (http://smart.embl-heidelberg.de/) (Letunic et al., 2011). After manually removing incorrect and redundant predicted proteins, the WRKY gene members were finally identified in carrot. As a control, the grape protein sequences were downloaded from Phytozome (https://phytozome.jgi.doe.gov/pz/portal.html#), which were analyzed using the same method as described above. The deduced grape WRKY genes were named as VvWRKY1 to VvWRKY 59 according to Guo et al. (2014). The sequences of Arabidopsis WRKY genes were downloaded from TAIR (https:/...
Source: Frontiers in Genetics - Category: Genetics & Stem Cells Source Type: research