Genome-wide identification and comparative analysis of the WRKY gene family in aquatic plants and their response to abiotic stresses in giant duckweed (Spirodela polyrhiza)

WRKY is one of the largest transcription factor families across higher plant species and is involved in important biological processes and plant responses to various biotic/abiotic stresses. However, only a few investigations on WRKYs have been conducted in aquatic plants. This study first systematically analyzed the gene structure, protein properties, and phylogenetic relationship of 693 WRKYs in nine aquatic and two wetland plants at the genome-wide level. The pattern of WRKY groups in two aquatic ferns provided new evidence for the origin and evolution of WRKY genes. ARE cis-regulatory elements show an unusual high frequency in the promoter region of WRKY genes, indicating the adaptation to the aquatic habitat in aquatic plants. The WRKY gene family experienced a series of gene loss events in aquatic plants, especially group III. Further studies were conducted on the interaction network of SpWRKYs, their target genes, and non-coding RNAs. The expression profile of SpWRKYs under phosphate starvation, cold, and submergence conditions revealed that most SpWRKYs are involved in the response to abiotic stresses. Our investigations lay the foundation for further study on the mechanism of WRKYs responding to abiotic stresses in aquatic plants.