Genome-Wide Identification of the Q-type C2H2 Zinc Finger Protein Gene Family and Expression Analysis under Abiotic Stress in Lotus (Nelumbo nucifera)

Abstract

Abstract Background Q-type C2H2 zinc finger proteins (ZFPs) play an important role in plant growth development and environmental stress responses. Although the Q-type C2H2 gene family has been identified in some plants, limited reports has been carried out it in lotus (Nelumbo nucifera). Results In this study, we identified 45 Q-type NnZFP members in lotus. Based on the phylogenetic tree, these Q-type NnZFP gene family members were divided into 4 groups, including C1-1i, C1-2i, C1-3i and C1-4i. Promoter cis-acting elements analysis indicated that most Q-type NnZFP gene family members in lotus are associated with response to abiotic stresses. Through collinearity analyses, no tandem duplication gene pairs and 14 segmental duplication gene pairs were identified, and it showed that duplication events play a key role in the expansion of the Q-type NnZFP gene family. The synteny results showed that 54 and 28 Q-type NnZFP genes were orthologous to Arabidopsis and rice, respectively. The expression patterns of these Q-type NnZFP genes showed that 30 Q-type NnZFP genes were expressed in at least one lotus tissue. Nn5g30550 showed relatively high expression levels in all tested tissues. The expression of 12 randomly selected gene from each phylogenetic clade was confirmed by qRT-PCR (quantitative real-time polymerase chain reaction), and it indicated that Q-type NnZFP genes are extensively involved in cadmium, drought, salt and cold stress responses. Among them, 11 genes responded to at least three different stress treatments, especially Nn2g12894 was induced by all four treatments. Conclusions These results could increase our understanding of the characterization of the Q-type NnZFP gene family and provide relevant information for further functional analysis of Q-type NnZFP genes in plant development, and abiotic stress tolerance in lotus.