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.
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Acknowledgments
The research was supported jointly by the National High Technology Research and Development Program of China (863 Program Grant No. 2011AA100202), National Natural Science Foundation of China (Grant No. 31200909; Grant No. 31100878), Zhejiang Provincial Natural Science Foundation of China (LQ12C06002), State Key Laboratory of Cotton Biology Open Fund (CB2013A02, CB2013B05) to Mingquan Ding, Junkang Rong and Aiqun Chen.
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M. Ding, J. Chen and Y. Jiang have contributed equally to this work.
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438_2014_904_MOESM2_ESM.tif
Supplemental Fig. 1 Multiple sequence alignment of WRKY domains in G. raimondii and G. aboreum. I1 and I2 represent the two WRKY domains of Group I WRKY genes (TIFF 2444 kb)
438_2014_904_MOESM3_ESM.tif
Supplemental Fig. 2 Gene structure of the WRKY genes in G. raimondii and G. arboreum. The red box indicated the WRKY domains and gray lines represented the introns separating the corresponding WRKY domains. (TIFF 3667 kb)
438_2014_904_MOESM4_ESM.png
Supplemental Fig. 3 Phylogenetic tree of group I, IIb, IIc, IId WRKY genes of Arabidopsis, Cacao, G. raimondii, and Poplar (PNG 2469 kb)
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Ding, M., Chen, J., Jiang, Y. et al. Genome-wide investigation and transcriptome analysis of the WRKY gene family in Gossypium . Mol Genet Genomics 290, 151–171 (2015). https://doi.org/10.1007/s00438-014-0904-7
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DOI: https://doi.org/10.1007/s00438-014-0904-7