Genome-Wide Identification of WRKY Transcription Factors in the Asteranae

Abstract

The WRKY transcription factors family, which participates in many physiological processes in plants, constitutes one of the largest transcription factor families. The Asterales and the Apiales are two orders of flowering plants in the superorder Asteranae. Among the members of the Asterales, globe artichoke (Cynara cardunculus var. scolymus L.), sunflower (Helianthus annuus L.), and lettuce (Lactuca sativa L.) are important economic crops worldwide. Within the Apiales, ginseng (Panax ginseng C. A. Meyer) and Panax notoginseng (Burk.) F.H. Chen are important medicinal plants, while carrot (Daucus carota subsp. carota L.) has significant economic value. Research involving genome-wide identification of WRKY transcription factors in the Asterales and the Apiales has been limited. In this study, 490 WRKY genes, 244 from three species of the Apiales and 246 from three species of the Asterales, were identified and categorized into three groups. Within each group, WRKY motif characteristics and gene structures were similar. WRKY gene promoter sequences contained light responsive elements, core regulatory elements, and 12 abiotic stress cis-acting elements. WRKY genes were evenly distributed on each chromosome. Evidence of segmental and tandem duplication events was found in all six species in the Asterales and the Apiales, with segmental duplication inferred to play a major role in WRKY gene evolution. Among the six species, we uncovered 54 syntenic gene pairs between globe artichoke and lettuce. The six species are thus relatively closely related, consistent with their traditional taxonomic placement in the Asterales. This study, based on traditional species classifications, was the first to identify WRKY transcription factors in six species from the Asteranae. Our results lay a foundation for further understanding of the role of WRKY transcription factors in species evolution and functional differentiation.

Genome-Wide Analysis, Characterization, and Expression Profile of the Basic Leucine Zipper Transcription Factor Family in Pineapple

“…TFs act as the key controller of major developmental processes and have indispensable roles in a variety of biological processes [51][52][53]. The transcriptional regulation of gene expression affects many important cellular processes, such as morphogenesis, environmental stress responses, and signal transduction [54].…”

Genome-wide characterization of WRKY gene family in Helianthus annuus L. and their expression profiles under biotic and abiotic stresses

“…In our study, we used "HA412.v1.1.bronze" database to search WRKY genes as support and addition to the previous works. Indeed, we found 89 WRKY genes which have corresponding genes in the results of Guo et al [20] and Liu et al [21], and we discovered another WRKY gene (HaWRKY51) which was neglected in their works. Multiple protein sequence alignments revealed domain variations in common sunflower WRKY family.…”

Genome-Wide Identification of WRKY Genes in Artemisia annua: Characterization of a Putative Ortholog of AtWRKY40

“…Large and variable numbers of WRKY TFs have been found in different plant species, likely reflecting their complex role in plant growth and response to abiotic and biotic stress [48]. Recently, WRKY transcription factors from sequenced genomes of six species of the superorder Asteranae were identified, and phylogenetic relationships, gene structures, cis-acting elements, and WRKY gene duplication events analyzed [49]. This analysis did not include A. annua, whose genome is also currently available [33].…”

“…Based on the whole amino acid sequence, the 122 AaWRKY were classified within the three main phylogenetic groups I, II, and III, with the second group further categorized into five subgroups (IIa-IIe) [34]. The WRKY family is significantly expanded in A. annua with respect to other Asteraceae species like L. sativa, Daucus carota, and Panax ginseng that have a number of WRKY genes comparable to Arabidopsis (ranging from 56 to 74) [49]. We focused our attention on the group IIa, to which the cloned AaWRKY40 gene belongs.…”