Genome-Wide Identification, Phylogenetic and Expression Pattern Analysis of GATA Family Genes in Cucumber (Cucumis sativus L.)

Abstract

GATA transcription factors are a class of transcriptional regulatory proteins that contain a characteristic type-IV zinc finger DNA-binding domain, which play important roles in plant growth and development. The GATA gene family has been characterized in various plant species. However, GATA family genes have not been identified in cucumber. In this study, 26 GATA family genes were identified in cucumber genome, whose physicochemical characteristics, chromosomal distributions, phylogenetic tree, gene structures conserved motifs, cis-regulatory elements in promoters, homologous gene pairs, downstream target genes were analyzed. Tissue expression profiles of cucumber GATA family genes exhibited that 17 GATA genes showed constitutive expression, and some GATA genes showed tissue-specific expression patterns. RNA-seq analysis of green and virescent leaves revealed that seven GATA genes might be involved in the chloroplast development and chlorophyll biosynthesis. Importantly, expression patterns analysis of GATA genes in response to abiotic and biotic stresses indicated that some GATA genes respond to either abiotic stress or biotic stress, some GATA genes such as Csa2G162660, Csa3G017200, Csa3G165640, Csa4G646060, Csa5G622830 and Csa6G312540 were simultaneously functional in resistance to abiotic and biotic stresses. Overall, this study will provide useful information for further analysis of the biological functions of GATA factors in cucumber.

Genome-wide identification and characterization of GATA family genes in wheat

“…GATA genes in subfamily II may be associated with flowering and also in response to abiotic stresses. Expression pattern analysis exhibit that GATA genes respond to diverse abiotic stresses, such as high temperature, salinity, cold, and drought treatments in rice, Brassica juncea , Brassica napus , Cucumis sativus , and pepper [ 17 , 18 , 48 , 55 , 56 ]. In Arabidopsis , GNC and GNL (ortholog of T aGATA38 ) were associated with germination, bloom and cold stress [ 49 ].…”

“…The first GATA factor NTL1 was found in tobacco ( Nicotiana tabacum ), which was a homolog of NIT2 form Neurospora crassa [ 10 ]. The GATA family gene was successively identified in a number of plants, such as Arabidopsis thaliana [ 4 ] , Oryza sativa [ 11 , 12 ], Glycine max [ 13 , 14 ], Brachypodium distachyon [ 15 , 16 ], Capsicum annuum [ 17 ], Cucumis sativus [ 18 ], Gossypium genus [ 19 ] and so on. In plants, all GATA factors are featured with one single zinc finger domain with 18 or 20 residues.…”

“…There were 30 GATA genes in Arabidopsis , 28 in rice, 35 in apple, and 64 in soybean according to Genome-wide analyses [ 4 , 13 , 20 ]. Plant GATA TFs have various roles like the chloroplast development [ 21 ], photosynthesis and growth [ 22 , 23 ], seed dormancy [ 24 ], host immune response [ 25 ], Grain shape [ 12 ], and abiotic stress [ 18 , 26 , 27 ]. In Arabidopsis , GATA12 are involved in primary seed dormancy [ 24 ].…”

Identification of GATA Transcription Factors in Brachypodium distachyon and Functional Characterization of BdGATA13 in Drought Tolerance and Response to Gibberellins

“…GATA TFs also respond to abiotic and biotic stresses. Expression profiles analysis show that rice, Brassica juncea , Cucumis sativus , and pepper GATA genes are in response to different abiotic stresses, including high temperature, salinity, cold, and drought treatments ( Bhardwaj et al, 2015 ; Gupta et al, 2017 ; Yu et al, 2021 ; Zhang K. et al, 2021 ). Arabidopsis GNC and GNL participate in cold stress response ( Richter et al, 2013a ); overexpression of OsGATA16 in rice improves cold tolerance ( Zhang H. et al, 2021 ); overexpression of OsGATA8 in rice improves drought tolerance ( Nutan et al, 2020 ); and overexpression of SlGATA17 improves drought tolerance in tomato ( Zhao et al, 2021 ).…”

Genome‐wide characterization and expression analysis of GATA transcription factors under combination of light wavelengths and drought stress in potato

“…The GATA transcription factor family is actively involved in light response and abiotic stress mechanisms, exhibiting high conservation across eukaryotes. Identified by a characteristic type IV zinc finger domain (CX 2 CX 17‐20 CX 2 C, where C represents cysteine and X is any amino acid) and a nearby basic region, GATA factors were first identified in tobacco (Daniel‐Vedele & Caboche, 1993 ) and have been extensively studied in various plant species, Arabidopsis thaliana (Kim, Xi, & Park, 2021 ; Teakle & Gilmartin, 1998 ), rice (Reyes et al, 2004 ), poplar (An et al, 2014 ), Noccaea caerulescens (Milner et al, 2014 ), soybean (Zhang et al, 2015 ), apple (Chen et al, 2017 ), grape (Zhang et al, 2018 ), Moso bamboo (Wang et al, 2019 ), Brachypodium distachyon (Peng et al, 2021 ), poplar (Kim, Xi, Park, Yun, & Park, 2021 ), cucumber (Zhang et al, 2021 ), potato (Yu, Chang, et al, 2021 ), wheat (Du et al, 2022 ; Feng et al, 2022 ), and foxtail millet (Lai et al, 2022 ). The GATA transcription factor‐binding cis ‐elements are commonly found in the promoters of genes associated with light and circadian rhythms, which are crucial for plant growth and development (Argüello‐Astorga & Herrera‐Estrella, 1998 ; Manfield et al, 2007 ).…”