Genome-wide identification of Tomato Golden 2-Like transcription factors and abiotic stress related members screening

Abstract

Background Golden 2-Like (G2-like) transcription factors play an important role in plant development. However, the roles of these G2-like regulatory genes in response to abiotic stresses in tomato are not well understood. Results In this study, we identified 66 putative G2-like genes in tomato (Solanum lycopersicum) and classified them into 5 groups (I to V) according to gene structure, motif composition and phylogenetic analysis. The G2-like genes were unevenly distributed across all 12 chromosomes. There were nine pairs of duplicated gene segments and four tandem duplicated SlGlk genes. Analysis of the cis-regulatory elements (CREs) showed that the promoter regions of SlGlks contain many kinds of stress- and hormone-related CREs. Based on RNA-seq, SlGlks were expressed in response to three abiotic stresses. Thirty-six differentially expressed SlGlks were identified; these genes have multiple functions according to Gene Ontology (GO) analysis and are enriched mainly in the zeatin biosynthesis pathway. Further studies exhibited that silencing SlGlk16 in tomato would reduce drought stress tolerance by earlier wilted, lower superoxide dismutase (SOD), peroxidase (POD) activities, less Pro contents and more MDA contents. Conclusions Overall, the results of this study provide comprehensive information on G2-like transcription factors and G2-like genes that may be expressed in response to abiotic stresses.

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

“…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.…”

Genome-Wide Identification and Characterization of G2-Like Transcription Factor Genes in Moso Bamboo (Phyllostachys edulis)

“…The GLK transcription factor, which is a member of the newly classified GARP superfamily [ 14 ], plays an essential role in the formation and development of chloroplasts [ 11 , 47 ]. As reported in previous studies, detailed features and functions of GLK genes have been uncovered in Arabidopsis [ 6 ], maize [ 22 ], tobacco [ 24 ], and tomato [ 23 ]. However, little was known about the members of the moso bamboo GLK family until now.…”

“…Moso bamboo ( Phyllostachys edulis ) is a rapidly growing forest product that is widely used to manufacture paper, art ware, and food resources, with multiple economic, ecological, and cultural values in China and many other countries, sees a possibility for gene identification and function analysis that will help with it contributing on an even wider spectrum with the completion of the genome sequence [ 6 , 20 , 21 ]. The GLK gene family, previously identified and described within certain plants, for example, maize [ 22 ], Arabidopsis [ 6 ], tomato [ 23 ], and tobacco [ 24 ]. However, there are scarcely any reports on the characteristics and functions of GLKs in Phyllostachys edulis .…”

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 ].…”