Comparative Genomic Analysis Reveals Extensive Genetic Variations of WRKYs in Solanaceae and Functional Variations of CaWRKYs in Pepper

Abstract

As a conserved protein family, WRKY has been shown to be involved in multiple biological processes in plants. However, the mechanism of functional diversity for WRKYs in pepper has not been well elucidated. Here, a total of 223 WRKY members from solanaceae crops including pepper, tomato and potato, were analyzed using comparative genomics. A tremendous genetic variation among WRKY members of different solanaceous plants or groups was demonstrated by the comparison of some WRKY features, including number/size, group constitution, gene structure, and domain composition. The phylogenetic analysis showed that except for the known WRKY groups (I, IIa/b/c/d/e and III), two extra WRKY subgroups specifically existed in solanaceous plants, which were named group IIf and group IIg in this study, and their genetic variations were also revealed by the characteristics of some group IIf and IIg WRKYs. Except for the extensive genetic variations, certain degrees of conservatism for solanaceae WRKYs were also revealed. Moreover, the variant zinc-finger structure (CX 4,7 CX 22-24 HXC) in group III of solanaceae WRKYs was identified. Expression profiles of CaWRKY genes suggested their potential roles in pepper development and stress responses, and demonstrated a functional division pattern for pepper CaWRKYs. Furthermore, functional analysis using virus induced gene silencing (VIGS) revealed critical roles of two CaWRKYs (CaWRKY45 and CaWRKY58) in plant responses to disease and drought, respectively. This study provides a solid foundation for further dissection of the evolutionary and functional diversity of solanaceae WRKYs in crop plants.

Identification of WRKY transcription factors associated with leaf and corolla senescence in Petunia hybrida

“…S1). Findings in PhWRKYs were in accordance with previous works describing the WRKY family in different species of the Solanaceae family, including potato, pepper, eggplant, and tomato (Huang et al 2012;Yang et al 2015;Cheng et al 2016;Zhang et al 2017;Cheng et al 2019) and species of other families like Arabidopsis, carrot, rice, and Brachypodium distachyon (Wu et al 2005;Rushton et al 2010;Tripathi et al 2012;Li et al 2016). Moreover, almost all senescence-associated PhWRKYs showed the most conserved WRKYGQK heptapeptide sequence, and only one member of the subgroup IIc showed a variation in this sequence (PhWRKY051).…”

“…This fact could explain the reduction in the number of WRKYs identi ed in petunia when compared to Arabidopsis. In accordance, a total of 81 members were identi ed in tomato and potato, while a signi cantly lower number (65) was identi ed in pepper (Cheng et al 2019). Moreover, the total number of WRKY members in the parental species of P. hybrida has not been assessed yet (Bombarely et al 2016).…”

“…The recovered sequences from the parental species showed scores and e-values consistently similar to those obtained for P. hybrida sequences (Supplementary Table S3). The total number of WRKYs described among different species, including those within the Solanaceae family, is variable (Cheng et al, 2019). This fact could explain the reduction in the number of WRKYs identi ed in petunia when compared to Arabidopsis.…”

WRKY genes family study reveals tissue-specific and stress-responsive TFs in wild potato species

“…Group II WRKYs can be divided into five subGroups (IIa-IIe) 10 . It is well recognized that Group I WRKY members are the evolutionary ancestors of the other WRKYs and that they exist only in lower plants 11,12 . The complexity of this gene family involves different molecular levels, from the transcriptional self-regulation through microRNAs to post-transcriptional events, such as alternative splicing, post-translational regulation through ubiquitin proteasome system and MAPK cascade 9 .…”

“…Despite this, to date no studies have examined WRKY gene family components and their different characteristics in wild potato species. A few data on this gene family are available only in the cultivated potato, where Zhang et al 21 , Liu et al 22 and Cheng et al 12 identified 79, 82 and 81 StWRKYs, respectively. Previously, Dellagi et al 23 identified StWRKY1 as a good candidate for functional studies, and Shahzad et al 24 overexpressed it in potato.…”