| Summary: | 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, <i>Arabidopsis thaliana</i>. 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 <i>RKD</i> genes, the <i>NLP</i> genes were just upregulated in nitrate response and nodulation. Moreover, nodule-specific <i>NLP</i> genes of some nodulating NFC species may have a common ancestor (OG0002084) with <i>AtNLP</i> genes in <i>A. thaliana</i>. Further, co-expression networks of <i>A.thaliana</i> under N-starvation and N-supplementation conditions revealed that there is a higher correlation between expression of <i>AtNLP</i> genes and symbiotic genes during N-starvation. In <i>P. vulgaris</i>, we confirmed that N-starvation stimulated nodulation by regulating expression of <i>PvNLP2</i>, closely related to <i>AtNLP6</i> and <i>AtNLP7</i> with another common origin (OG0004041). Taken together, we concluded that different origins of the <i>NLP</i> 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 <i>NLP</i> genes and their differential regulation in nitrate response of <i>A. thaliana</i> and nodulation of NFC.
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