Genome-wide investigation and transcriptome analysis of the WRKY gene family in Gossypium

Abstract

WRKY transcription factors play important roles in various stress responses in diverse plant species. In cotton, this family has not been well studied, especially in relation to fiber development. Here, the genomes and transcriptomes of Gossypium raimondii and Gossypium arboreum were investigated to identify fiber development related WRKY genes. This represents the first comprehensive comparative study of WRKY transcription factors in both diploid A and D cotton species. In total, 112 G. raimondii and 109 G. arboreum WRKY genes were identified. No significant gene structure or domain alterations were detected between the two species, but many SNPs distributed unequally in exon and intron regions. Physical mapping revealed that the WRKY genes in G. arboreum were not located in the corresponding chromosomes of G. raimondii, suggesting great chromosome rearrangement in the diploid cotton genomes. The cotton WRKY genes, especially subgroups I and II, have expanded through multiple whole genome duplications and tandem duplications compared with other plant species. Sequence comparison showed many functionally divergent sites between WRKY subgroups, while the genes within each group are under strong purifying selection. Transcriptome analysis suggested that many WRKY genes participate in specific fiber development processes such as fiber initiation, elongation and maturation with different expression patterns between species. Complex WRKY gene expression such as differential Dt and At allelic gene expression in G. hirsutum and alternative splicing events were also observed in both diploid and tetraploid cottons during fiber development process. In conclusion, this study provides important information on the evolution and function of WRKY gene family in cotton species.

Regulation of cotton (Gossypium hirsutum) drought responses by mitogen‐activated protein (MAP) kinase cascade‐mediated phosphorylation of GhWRKY59

“…S2a), placing GhWRKY59 in the group III WRKY protein family. In G. raimondii , there are 112 putative WRKYs, which can be divided into three groups with 20 in group I, 78 in group II, and 14 in group III (Ding et al ., ). The closest orthologs of GhWRKY59 are populus ( Populus tomentosa ) PtWRKY27, cocoa ( Theobroma cacao ) TcWRKY30, soybean ( Glycine max ) GmWRKY53, tobacco ( Nicotiana tabacum ) NtWRKY53, Arabidopsis AtWRKY30, and rice ( Oryza sativa ) OsWRKY54 (Fig.…”

Genome-wide identification of the potato WRKY transcription factor family

“…Many studies have shown that WRKY gene family members are related to plant development processes, such as fiber development [16] and leaf senescence in cotton [17]. Some researchers showed that the WRKY gene family members were related to development of the embryo and anther [18, 19].…”

Recent Developments in Fiber Genomics of Tetraploid Cotton Species

“…The association of WRKY allelic gene expression (D t and A t ) in G. hirsutum and alternative splicing events were likewise seen in both diploid and tetraploid cotton during the developmental stage of the fiber. In summary, this study provided new results for the evolution and role of WRKY gene family in cotton species [91].…”