Comprehensive Genomic Analysis of G2-like Transcription Factor Genes and Their Role in Development and Abiotic Stresses in Arabidopsis

Abstract

GOLDEN2-LIKE (GLK) transcription factors are a subfamily of GARP family transcription factors, which play an essential function in plant growth and development as well as stress response during abiotic and biotic stress conditions. This study reports GLK genes in the Arabidopsis thaliana genome in-depth and identified 55 AtGLK genes in the Arabidopsis genome. Phylogenetic analyses resolved these GLK gene clusters into seven groups. A Ka/Ks ratios analysis indicated that they had experienced purifying selection. Many essential cis elements are present in the promoter regions of AtGLK genes associated with plant hormones, light, and stress. The expression profile from RNA-Seq data revealed that 29.1% of them had relatively high expression in all tested tissues or organs, indicating their crucial housekeeping function in plant growth and development. However, many other GLK members were selectively expressed in particular tissues or organs. In silico study of the transcriptional regulation of AtGLKs indicated that it is strongly regulated by cold, drought, osmotic, salt, and metal ion stressors. Our research provides essential information for the functional studies of each GLK gene in different species in the future.

Genome-wide characterization and analysis of Golden 2-Like transcription factors related to leaf chlorophyll synthesis in diploid and triploid Eucalyptus urophylla

“…The synteny relationships of GLK genes between E. grandis and other species showed that the number of homologous gene pairs between E. grandis and dicotyledons was much more than that between E. grandis and monocotyledons, indicating that GLK gene family has been amplified after differentiation between dicotyledon and monocotyledon ( Figure 2 ). The EgrGLK genes were classified into seven groups based on a phylogenetic analysis ( Figure 3 ), which was consistent with the classification of GLK genes in Arabidopsis ( Alam et al, 2022 ). This result indicated that, although some EgrGLK genes were lost during evolution, the sufficient genetic diversity has been retained in E. grandis .…”

“…In this study, 40 EgrGLK genes were identified in the E. grandis genome (Supplementary Table S2). The number of EgrGLK genes was less than the number of GLK genes identified in Arabidopsis (55), maize (59), and tomato (66) (Liu et al, 2016;Alam et al, 2022;Wang et al, 2022). It was suspected that some EgrGLK genes were lost during evolution (Du et al, 2022).…”

“…To identify the GLK genes of E. grandis , genomic data were downloaded from the Phytozome database. 1 Using published GLK protein sequences from Arabidopsis , maize, and tomato as query sequences ( Liu et al, 2016 ; Alam et al, 2022 ; Wang et al, 2022 ), the GLK protein sequences in the E. grandis reference genome were identified with the BLASTP tool ( E -value: 1e −5 ). The identified sequences were submitted to the SMART online tool 2 and the NCBI Web CD-Search Tool 3 for further confirmation of GLK proteins.…”

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

“…Salinity stress is one of the major abiotic stresses limiting plant growth and productivity, it also suppresses the growth of S. polyrhiza [ 60 ]. There are many reports of the GARP genes that responded to salt stress, such as AtGLK2/5/8/20/23/26/34/43/46 in A. thaliana [ 11 ], ZeGLK3 in Z. mays [ 43 ], 27 SiGLK genes in S. lycopersicum [ 61 ], and GhGLK55/120 in G. hirsutum [ 40 ]. In our study, we found that the expression of SpGLK25 was downregulated under salt stress, which helps to explain why the salt stress affects N/P uptake, and growth rate in plants [ 60 ].…”

“…GLK TFs play important roles in biotic and abiotic stresses, such as pathogen infection, salt stress, drought, and nutrient deficiency. AtGLK1 regulates genes that involved in disease resistance and effect on different pathogen [ 10 ], nine AtGLK genes were responded to salt stress in A. thaliana [ 11 ]. Both of Phosphorus Starvation Response 1 (Psr1) in C. reinhardtii and Phosphate Starvation Response 1 (PHR1) in A. thaliana play the central regulatory roles in inorganic phosphate (Pi) sensing system [ 12 , 13 ].…”