In silico identification and characterization of the WRKY gene superfamily in pepper (Capsicum annuum L.)

Abstract

The WRKY family is one of the most important transcription factor families in plants, involved in the regulation of a broad range of biological roles. The recent releases of whole-genome sequences of pepper (Capsicum annuum L.) allow us to perform a genome-wide identification and characterization of the WRKY family. In this study, 61 CaWRKY proteins were identified in the pepper genome. Based on protein structural and phylogenetic analyses, these proteins were classified into four main groups (I, II, III, and NG), and Group II was further divided into five subgroups (IIa to IIe). Chromosome mapping analysis indicated that CaWRKY genes are distributed across all 12 chromosomes, although the location of four CaWRKYs (CaWRKY58-CaWRKY61) could not be identified. Two pairs of CaWRKYs located on chromosome 01 appear to be tandem duplications. Furthermore, the phylogenetic tree showed a close evolutionary relationship of WRKYs in three species from Solanaceae. In conclusion, this comprehensive analysis of CaWRKYs will provide rich resources for further functional studies in pepper.

Genome-wide identification of the potato WRKY transcription factor family

“…Through identification of tandem duplication was based on Cheng’s method and these closely genes were termed a cluster [3]. StWRKY genes formed in clusters on chromosome 3, 5, 8 and 12.…”

“…The software MapChart2.30 was used to map the gene locus on chromosomes. Tandem duplication of StWRKY s was identified according the method of Cheng [3]. Two or more WRKY genes within a distancs of 100 kb were regarded as tandem duplications [3, 34].…”

“…Tandem duplication of StWRKY s was identified according the method of Cheng [3]. Two or more WRKY genes within a distancs of 100 kb were regarded as tandem duplications [3, 34]. Information on segmental duplications was sourced from the PGDD website (http://chibba.agtec.uga.edu/duplication/), and segmental duplications were displayed using Circos software.…”

“…The WRKY domain is a highly conserved sequence of 60 amino acids [3], heptapeptide WRKYGQK which also has WRKYGKK, WKKYGQK, WRKYGQR, WRKYGEK and some other forms [4, 5], and a zinc finger structure. which is itself divided into two types, C2H2 and C2HC [6].…”

Identification and cloning of GOLDEN2-LIKE1 (GLK1), a transcription factor associated with chloroplast development in Brassica napus L.

“…Multiple alignment analysis was performed using BioEdit 7.0 with shading >80% threshold (Cheng et al, 2016). Using the neighbor-joining (NJ) method, a phylogenetic tree based on GLK1 amino acid sequences was constructed using the biosoftware Geneious Pro 4.8.5.…”