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 u...
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Language: | English |
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MDPI AG
2020-09-01
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Series: | Plants |
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Online Access: | https://www.mdpi.com/2223-7747/9/9/1178 |
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record_format |
Article |
collection |
DOAJ |
language |
English |
format |
Article |
sources |
DOAJ |
author |
Zhihua Wu Hong Liu Wen Huang Lisha Yi Erdai Qin Tiange Yang Jing Wang Rui Qin |
spellingShingle |
Zhihua Wu Hong Liu Wen Huang Lisha Yi Erdai Qin Tiange Yang Jing Wang Rui Qin Genome-Wide Identification, Characterization, and Regulation of RWP-RK Gene Family in the Nitrogen-Fixing Clade Plants RWP-RK nitrogen-fixing clade co-expression network evolution nodulation |
author_facet |
Zhihua Wu Hong Liu Wen Huang Lisha Yi Erdai Qin Tiange Yang Jing Wang Rui Qin |
author_sort |
Zhihua Wu |
title |
Genome-Wide Identification, Characterization, and Regulation of RWP-RK Gene Family in the Nitrogen-Fixing Clade |
title_short |
Genome-Wide Identification, Characterization, and Regulation of RWP-RK Gene Family in the Nitrogen-Fixing Clade |
title_full |
Genome-Wide Identification, Characterization, and Regulation of RWP-RK Gene Family in the Nitrogen-Fixing Clade |
title_fullStr |
Genome-Wide Identification, Characterization, and Regulation of RWP-RK Gene Family in the Nitrogen-Fixing Clade |
title_full_unstemmed |
Genome-Wide Identification, Characterization, and Regulation of RWP-RK Gene Family in the Nitrogen-Fixing Clade |
title_sort |
genome-wide identification, characterization, and regulation of rwp-rk gene family in the nitrogen-fixing clade |
publisher |
MDPI AG |
series |
Plants |
issn |
2223-7747 |
publishDate |
2020-09-01 |
description |
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. |
topic |
RWP-RK nitrogen-fixing clade co-expression network evolution nodulation |
url |
https://www.mdpi.com/2223-7747/9/9/1178 |
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spelling |
doaj-9ca73e2cbdf64196ba315f3f1102cbb32020-11-25T02:36:02ZengMDPI AGPlants2223-77472020-09-0191178117810.3390/plants9091178Genome-Wide Identification, Characterization, and Regulation of RWP-RK Gene Family in the Nitrogen-Fixing CladeZhihua Wu0Hong Liu1Wen Huang2Lisha Yi3Erdai Qin4Tiange Yang5Jing Wang6Rui Qin7Hubei Provincial Key Laboratory for Protection and Application of Special Plant Germplasm in Wuling Area of China & Key Laboratory of State Ethnic Affairs Commission for Biological Technology, College of Life Sciences, South-Central University for Nationalities, Wuhan 430074, ChinaHubei Provincial Key Laboratory for Protection and Application of Special Plant Germplasm in Wuling Area of China & Key Laboratory of State Ethnic Affairs Commission for Biological Technology, College of Life Sciences, South-Central University for Nationalities, Wuhan 430074, ChinaHubei Provincial Key Laboratory for Protection and Application of Special Plant Germplasm in Wuling Area of China & Key Laboratory of State Ethnic Affairs Commission for Biological Technology, College of Life Sciences, South-Central University for Nationalities, Wuhan 430074, ChinaHubei Provincial Key Laboratory for Protection and Application of Special Plant Germplasm in Wuling Area of China & Key Laboratory of State Ethnic Affairs Commission for Biological Technology, College of Life Sciences, South-Central University for Nationalities, Wuhan 430074, ChinaHubei Provincial Key Laboratory for Protection and Application of Special Plant Germplasm in Wuling Area of China & Key Laboratory of State Ethnic Affairs Commission for Biological Technology, College of Life Sciences, South-Central University for Nationalities, Wuhan 430074, ChinaHubei Provincial Key Laboratory for Protection and Application of Special Plant Germplasm in Wuling Area of China & Key Laboratory of State Ethnic Affairs Commission for Biological Technology, College of Life Sciences, South-Central University for Nationalities, Wuhan 430074, ChinaInstitute of Food and Nutrition Development, Ministry of Agriculture, Chinese Academy of Agricultural Sciences, Beijing 100081, ChinaHubei Provincial Key Laboratory for Protection and Application of Special Plant Germplasm in Wuling Area of China & Key Laboratory of State Ethnic Affairs Commission for Biological Technology, College of Life Sciences, South-Central University for Nationalities, Wuhan 430074, ChinaRWP-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.https://www.mdpi.com/2223-7747/9/9/1178RWP-RKnitrogen-fixing cladeco-expression networkevolutionnodulation |