Identification and expression analysis of GARP superfamily genes in response to nitrogen and phosphorus stress in Spirodela polyrhiza

Xuyao Zhao; Jingjing Yang; Xiaozhe Li; Gaojie Li; Zuoliang Sun; Yan Chen; Yimeng Chen; Manli Xia; Yixian Li; Lunguang Yao; Hongwei Hou

doi:10.1186/s12870-022-03696-5

Identification and expression analysis of GARP superfamily genes in response to nitrogen and phosphorus stress in Spirodela polyrhiza

BMC Plant Biol. 2022 Jun 25;22(1):308. doi: 10.1186/s12870-022-03696-5.

Authors

Xuyao Zhao¹, Jingjing Yang¹, Xiaozhe Li¹, Gaojie Li¹, Zuoliang Sun^{1

2}, Yan Chen^{1

2}, Yimeng Chen^{1

2}, Manli Xia^{1

2}, Yixian Li^{1

2}, Lunguang Yao³, Hongwei Hou⁴

Affiliations

¹ The State Key Laboratory of Freshwater Ecology and Biotechnology, The Key Laboratory of Aquatic Biodiversity and Conservation of Chinese Academy of Sciences, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072, China.
² University of Chinese Academy of Sciences, Beijing, 100049, China.
³ Henan Key Laboratory of Ecological Security for Water Source Region of Mid-Line of South-to-North Diversion Project of Henan Province, Collaborative Innovation Center of Water Security for Water Source Region of Mid-Line of South-to-North Diversion Project of Henan Province, Nanyang Normal University, Nanyang, 473061, China.
⁴ The State Key Laboratory of Freshwater Ecology and Biotechnology, The Key Laboratory of Aquatic Biodiversity and Conservation of Chinese Academy of Sciences, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072, China. houhw@ihb.ac.cn.

Abstract

Background: GARP transcription factors perform critical roles in plant development and response to environmental stimulus, especially in the phosphorus (P) and nitrogen (N) sensing and uptake. Spirodela polyrhiza (giant duckweed) is widely used for phytoremediation and biomass production due to its rapid growth and efficient N and P removal capacities. However, there has not yet been a comprehensive analysis of the GRAP gene family in S. polyrhiza.

Results: We conducted a comprehensive study of GRAP superfamily genes in S. polyrhiza. First, we investigated 35 SpGARP genes which have been classified into three groups based on their gene structures, conserved motifs, and phylogenetic relationship. Then, we identified the duplication events, performed the synteny analysis, and calculated the K_a/K_s ratio in these SpGARP genes. The regulatory and co-expression networks of SpGARPs were further constructed using cis-acting element analysis and weighted correlation network analysis (WGCNA). Finally, the expression pattern of SpGARP genes were analyzed using RNA-seq data and qRT-PCR, and several NIGT1 transcription factors were found to be involved in both N and P starvation responses.

Conclusions: The study provides insight into the evolution and function of GARP superfamily in S. polyrhiza, and lays the foundation for the further functional verification of SpGARP genes.

Keywords: Expression pattern; GARP superfamily; NIGT1/HRS1/HHO transcription factor; PHR transcription factor; Spirodela polyrhiza.

MeSH terms

Araceae* / genetics
Gene Expression Regulation, Plant
Nitrogen / metabolism
Phosphorus* / metabolism
Phylogeny
Transcription Factors / genetics
Transcription Factors / metabolism

Substances

Transcription Factors
Phosphorus
Nitrogen

Abstract

MeSH terms

Substances

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