Genome-Wide Identification and Expression Analysis of WRKY Gene Family in Nelumbo nucifera

Abstract

Abstract WRKY transcription factors play important roles in various stress responses in diverse plant species. We identified a total of 54 WRKY genes (NnWKRY) in the lotus genome. All NnWRKY genes were found to scattered in 14 of 50 scaffolds. A phylogenetic tree was constructed and 54 NnWKRY genes were classified into 5 separate monophyletic groups. Gene structure analysis indicate that WRKY IIa might be the most ancestral in lotus WKRY gene family. dN/dS ratios were always less than 1 for both WKRY domains and higher than 1 in amino acid sequence outside the domain, implying the relaxed purifying or positive selection on this region. Six amino acid residues were identified in the NnWKRY domain, which presumably have contributed to the functional divergence of lotus WKRY genes. We tested two pairs of codon substitution models to test positive selection using likelihood ratio test and one positive selection site (625G, corresponding to NNU_013102) were identified. Moreover, gene conversion events might have played significant role during the evolutionary history of lotus WRKY family. Expression profiling revealed that NnWRKY genes might primarily have functions in sink tissues. Several NnWRKY genes were found to be changed obviously and might have roles in rhizome development, energy metabolism and stress responses. The present study provides a foundation for further functional studies of NnWKRYs in lotus.