Genome-wide analysis of the WRKY gene family in cotton

Abstract

WRKY proteins are major transcription factors involved in regulating plant growth and development. Although many studies have focused on the functional identification of WRKY genes, our knowledge concerning many areas of WRKY gene biology is limited. For example, in cotton, the phylogenetic characteristics, global expression patterns, molecular mechanisms regulating expression, and target genes/pathways of WRKY genes are poorly characterized. Therefore, in this study, we present a genome-wide analysis of the WRKY gene family in cotton (Gossypium raimondii and Gossypium hirsutum). We identified 116 WRKY genes in G. raimondii from the completed genome sequence, and we cloned 102 WRKY genes in G. hirsutum. Chromosomal location analysis indicated that WRKY genes in G. raimondii evolved mainly from segmental duplication followed by tandem amplifications. Phylogenetic analysis of alga, bryophyte, lycophyta, monocot and eudicot WRKY domains revealed family member expansion with increasing complexity of the plant body. Microarray, expression profiling and qRT-PCR data revealed that WRKY genes in G. hirsutum may regulate the development of fibers, anthers, tissues (roots, stems, leaves and embryos), and are involved in the response to stresses. Expression analysis showed that most group II and III GhWRKY genes are highly expressed under diverse stresses. Group I members, representing the ancestral form, seem to be insensitive to abiotic stress, with low expression divergence. Our results indicate that cotton WRKY genes might have evolved by adaptive duplication, leading to sensitivity to diverse stresses. This study provides fundamental information to inform further analysis and understanding of WRKY gene functions in cotton species.

Genome-wide analysis of WRKY gene family in the sesame genome and identification of the WRKY genes involved in responses to abiotic stresses

“…Most SiWRKY genes were highly expressed in roots, whereas a few SiWRKY genes were expressed in developing seeds. This is consistent with observations made in other plants, including rice [18], cucumber [33], grape [42], apple [13], cassava [30], cotton [43], physic nut [41], and cabbage [44]. Our results revealed that SiWRKY genes are expressed tissuespecifically and the high expression levels observed in roots might reflect their roles in responses to abiotic and biotic stresses that first affect plants below ground.…”

Evolutionary Dynamics of the Leucine-Rich Repeat Receptor-Like Kinase (LRR-RLK) Subfamily in Angiosperms

“…NAC transcription factors; Shang et al, 2013) or by a combination of segmental duplications (SDs) and tandem duplications (TDs; e.g. WRKY transcription factors; Dou et al, 2014). For apple (most recent WDG after the divergence for peach [Prunus persica] according to Verde et al [2013]), a recent study on nucleotide-binding site LRR genes showed that they also stem mostly from SDs and TDs (Arya et al, 2014).…”

Cloning, Characterization and Expression Analysis of GbWRKY11, a Novel Transcription Factor Gene in Ginkgo biloba

“…A large number of WRKY genes have been isolated and characterized in various plant species, such as in Arabidopsis (Eulgem et al, 2000), Zea mays (Wei et al, 2012), Gossypium (Dou et al, 2014), Medicago truncatula ( and Nan, 2014), Cucumis sativus (Ling et al, 2011), B. rapa , Vitis vinifera , Carica papaya (Pan and Jiang, 2014), Coffea arabica (Ramiro et al, 2010), Populus , Hevea brasiliensis , Coptis japonica (Kato et al, 2007), and Catharanthus roseus (Yang et al, 2013). However, knowledge on WRKYs of G. biloba remains limited.…”