Genome-Wide Identification, Characterization, and Regulation of RWP-RK Gene Family in the Nitrogen-Fixing Clade.

RWP-RK is a plant-specific family of transcription factors, involved in nitrate response, gametogenesis, and nodulation. However, genome-wide characterization, phylogeny, and the regulation of RWP-RK genes in the nodulating and non-nodulating plant species of nitrogen-fixing clade (NFC) are widely unknown. Therefore, we identified a total of 292 RWP-RKs, including 278 RWP-RKs from 25 NFC species and 14 RWP-RKs from the outgroup, . We classified the 292 RWP-RKs in two subfamilies: the NIN-like proteins (NLPs) and the RWP-RK domain proteins (RKDs). The transcriptome and phylogenetic analysis of RWP-RKs suggested that, compared to genes, the genes were just upregulated in nitrate response and nodulation. Moreover, nodule-specific genes of some nodulating NFC species may have a common ancestor (OG0002084) with genes in . Further, co-expression networks of under N-starvation and N-supplementation conditions revealed that there is a higher correlation between expression of genes and symbiotic genes during N-starvation. In , we confirmed that N-starvation stimulated nodulation by regulating expression of , closely related to and with another common origin (OG0004041). Taken together, we concluded that different origins of the genes involved in both N-starvation response and specific expression of nodulation would contribute to the evolution of nodulation in NFC plant species. Our results shed light on the phylogenetic relationships of genes and their differential regulation in nitrate response of and nodulation of NFC.