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

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 Ka/Ks 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.

Ammonium Uptake, Mediated by Ammonium Transporters, Mitigates Manganese Toxicity in Duckweed, Spirodela polyrhiza

“…The members of the NIGT1 (Nitrate-Inducible GARP-Type Transcriptional Repressor-1) subfamily in the superfamily of GARP transcription factors [ 59 ], participate in fine-tuning of gene expression in response to the plant nitrogen and phosphorus status [ 60 ]. The proteins bind to two types of cis -elements, GAATC and GAATATTC demonstrating dual modes of promoter recognition [ 61 , 62 ].…”

Genome-Scale Investigation of GARP Family Genes Reveals Their Pivotal Roles in Nutrient Stress Resistance in Allotetraploid Rapeseed

“…In this study, a total of 146 BnaGARPs were identified (Table S1). A previous study has revealed 56 GARPs in A. thaliana, 69 GARPs in Camellia sinensis, and 35 GARPs in S. polyrhiza [8,10,50], suggesting that the GARP TF family is ubiquitous in plants (Table S11). The GARP gene family in rapeseed is larger than those in other plant species, which might be due to complex whole genome duplication and subsequent evolution of the rapeseed genome.…”

Comprehensive transcriptomic meta-analysis unveils new responsive genes to methyl jasmonate and ethylene in Catharanthus roseus

“…GARP transcription factors assume crucial functions in plant growth and their reaction to environmental stimuli. For instance, GARP's NIGT1 genes respond to phosphorus (P) and nitrogen (N) stresses, with some being downregulated following nitrogen stresses (NS) treatment [ 62 ]. Additionally, B3 subfamily proteins within the ERF family are associated to the regulation of secondary metabolites [ 63 ].…”