Genome-wide characterization, expression profiling, and post-transcriptional study of GASA gene family

Rezaee, Sadra; Ahmadizadeh, Mostafa; Heidari, Parviz

doi:10.1016/j.genrep.2020.100795

Cited by 39 publications

(41 citation statements)

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“…The GASA proteins have low molecular weight with conserved GASA and cysteine domains. Our findings are in agreement with previous studies that revealed that GASA genes mostly exist in lower numbers, have low molecular weight, and are unequally distributed on chromosomes within genomes as reported for rice (9; Rezaee et al, 2020), Grapevine (14; Ahmad et al, 2020b), Arabidopsis (15; Fan et al, 2017), and tomato (19; Rezaee et al, 2020). However, a somewhat high number of GASA have also reported, such as in apple (26; Fan et al, 2017) and soybean (37; Ahmad et al, 2019).…”

Section: Discussionsupporting

confidence: 94%

“…GAST1 was the first gene identified among the GASA family’s genes in tomato (Shi et al, 1992). GASA proteins are comprised of three domains, including a signal peptide of up to 18–29 amino acids at the N-terminal, hydrophilic and high variable regions of up to 7–31 amino acids in the center, and a conserved domain at the C-terminal of up to 60 amino acids which mostly includes 12 cysteine residues (Rezaee et al, 2020; Silverstein et al, 2007; Zhang and Wang, 2008). This third domain of the C-terminal is the characteristics of all identified GASAs (Ahmad et al, 2019; Fan et al, 2017; Rezaee et al, 2020; Zhang and Wang, 2008).…”

Section: Introductionmentioning

confidence: 99%

“…Their roles have been stated in organ development (Fuente et al, 2006), lateral root development (Zimmermann et al, 2010), stem growth (Zhang et al, 2009), cell division (Nahirñak et al, 2012; Roxrud et al, 2007), fruit ripening and development (Moyano-Cañete et al, 2013), flowering time (Ahmad et al, 2019; Fan et al, 2017; Zhang et al, 2009), seed development (Ahmad et al, 2020b; Roxrud et al, 2007), and bud dormancy (Yang et al, 2019). The detailed expression analyses of various tissues of Arabidopsis, tomato, rice, soybean, and apple showed the tissue-specific expression of the GASA genes (Ahmad et al, 2019; Fan et al, 2017; Rezaee et al, 2020). For example, GASA genes in tomato, including Solyc11g011210 , Solyc12g089300 , and Solyc01g111075, showed high expression at the fruit-ripening stage, whereas Solyc03g113910 , Solyc01g111075 , Solyc06g069790 , and Solyc12g042500 showed high expression level at the flowering stage (Rezaee et al, 2020).…”

Section: Introductionmentioning

confidence: 99%

“…The detailed expression analyses of various tissues of Arabidopsis, tomato, rice, soybean, and apple showed the tissue-specific expression of the GASA genes (Ahmad et al, 2019; Fan et al, 2017; Rezaee et al, 2020). For example, GASA genes in tomato, including Solyc11g011210 , Solyc12g089300 , and Solyc01g111075, showed high expression at the fruit-ripening stage, whereas Solyc03g113910 , Solyc01g111075 , Solyc06g069790 , and Solyc12g042500 showed high expression level at the flowering stage (Rezaee et al, 2020). Moreover, some studies also showed the contrast effect of GASA proteins.…”

Section: Introductionmentioning

confidence: 99%

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TheGASAGene Family inTheobroma cacao: Genome wide Identification and Expression Analysis

Abdullah

Faraji

Mehmood

et al. 2021

Preprint

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The gibberellic acid-stimulated Arabidopsis (GASA/GAST) gene family is widely distributed in plants. The role of the GASA gene family has been reported previously in various physiological and biological processes, such as cell division, root and seed development, stem growth, and fruit ripening. These genes also provide resistance to abiotic and biotic stresses including antimicrobial, antiviral, and antifungal. Here, we report 17 tcGASA genes in Theobroma cacao L. distributed on six chromosomes. The gene structure, promoter-region sequences, protein structure, and biochemical properties, expression, and phylogenetics of all tcGASAs were analyzed. Phylogenetic analyses divided tcGASA proteins into five groups. The nine segmentally duplicating genes form four pairs and cluster together in phylogenetic tree. Purifying selection pressure was recorded on tcGASA, including duplicated genes. Several stress/hormone-responsive cis-regulatory elements were also recognized in the promoter region of tcGASAs. Differential expression analyses revealed that most of the tcGASA genes showed elevated expression in the seeds (cacao food), implying their role in seed development. The black rod disease of genus Phytophthora caused up to 20–25% loss (700,000 metric tons) in world cacao production. The role of tcGASA genes in conferring fungal resistance was also explored based on RNAseq data against Phytophthora megakarya. The differential expression of tcGASA genes was recorded between the tolerant and susceptible cultivars of cacao plants, which were inoculated with the fungus for 24h and 72h. This differential expression indicating possible role of tcGASA genes to fungal resistant in cacao. Our findings provide new insight into the function, evolution, and regulatory system of the GASA family genes in T. cacao and provide new target genes for development of fungi-resistant cacao varieties in breeding programs.

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Section: Discussionsupporting

confidence: 94%

Section: Introductionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

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TheGASAGene Family inTheobroma cacao: Genome wide Identification and Expression Analysis

Abdullah

Faraji

Mehmood

et al. 2021

Preprint

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“…The modulation of gene expression in response to stresses is highly controlled by specific transcription factors (TFs), which simultaneously mediate the transcription of a vast number of downstream stress-responsive genes [3,4]. TFs have been extensively proposed to be significant regulatory proteins involved in modifying plant growth and the stress response [5,6]. Among the members of multiple TF groups, the members of the APETALA2/ethylene-responsive factor (AP2/ERF) superfamily have multiple functions in plant development and play roles in the biosynthesis of many key metabolites, providing the ability to address environmental stress [7].…”

Section: Introductionmentioning

confidence: 99%

The AP2/ERF Gene Family in Triticum durum: Genome-Wide Identification and Expression Analysis under Drought and Salinity Stresses

Faraji

Filiz

Kazemitabar

et al. 2020

Genes

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Members of the AP2/ERF transcription factor family play critical roles in plant development, biosynthesis of key metabolites, and stress response. A detailed study was performed to identify TtAP2s/ERFs in the durum wheat (Triticum turgidum ssp. durum) genome, which resulted in the identification of 271 genes distributed on chromosomes 1A-7B. By carrying 27 genes, chromosome 6A had the highest number of TtAP2s/ERFs. Furthermore, a duplication assay of TtAP2s/ERFs demonstrated that 70 duplicated gene pairs had undergone purifying selection. According to RNA-seq analysis, the highest expression levels in all tissues and in response to stimuli were associated with DRF and ERF subfamily genes. In addition, the results revealed that TtAP2/ERF genes have tissue-specific expression patterns, and most TtAP2/ERF genes were significantly induced in the root tissue. Additionally, 13 TtAP2/ERF genes (six ERFs, three DREBs, two DRFs, one AP2, and one RAV) were selected for further analysis via qRT-PCR of their potential in coping with drought and salinity stresses. The TtAP2/ERF genes belonging to the DREB subfamily were markedly induced under both drought-stress and salinity-stress conditions. Furthermore, docking simulations revealed several residues in the pocket sites of the proteins associated with the stress response, which may be useful in future site-directed mutagenesis studies to increase the stress tolerance of durum wheat. This study could provide valuable insights for further evolutionary and functional assays of this important gene family in durum wheat.

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GhGASA14 regulates the flowering time of upland cotton in response to GA3

Li,

Yuan,

Peng

et al. 2024

Plant Cell Rep

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The gibberellic acid-stimulated Arabidopsis (GASA), a gibberellin-regulated short amino acid family, has been extensively investigated in several plant species and found to be critical for plant growth and development. However, limited research has been reported in cotton. In this study, we identi ed 38 GhGASAs that were dispersed across 18 chromosomes in upland cotton, and all of these genes had a GASA core domain. Transcriptome expression patterns and qRT-PCR results revealed that GhGASA9 and GhGASA14 exhibited upregulated expression not only in the oral organs but also in the leaves of early-maturity cultivars. The two genes were further functionally characterized by virus-induced gene silencing (VIGS) and the budding and owering times after silencing the target genes were later than those of the control (TRV:00). Exogenous application of GA 3 made the owering period of the different fruiting branches more concentrated compared with that of the water-treated group (MOCK). Interestingly, allelic variation was detected in the coding sequence of GhGASA14 between early-maturing and late-maturing accessions, and the frequency of this favorable allele was greater in high-latitude cotton varieties than in low-latitude ones. Additionally, a signi cant linear relationship was observed between the expression level of GhGASA14 and owering time among the 12 upland cotton accessions. Taken together, these results indicated that GhGASA14 may positively regulate owering time and respond to GA 3 . These ndings could lead to the use of valuable genetic resources for breeding earlymaturing cotton varieties in the future. Key messageThe silencing of GhGASA14 and the identi cation of superior allelic variation in its coding region indicate that GhGASA14 may positively regulate owering and respond to GA3.

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Genome-wide characterization, expression profiling, and post-transcriptional study of GASA gene family

Cited by 39 publications

References 61 publications

TheGASAGene Family inTheobroma cacao: Genome wide Identification and Expression Analysis

TheGASAGene Family inTheobroma cacao: Genome wide Identification and Expression Analysis

The AP2/ERF Gene Family in Triticum durum: Genome-Wide Identification and Expression Analysis under Drought and Salinity Stresses

GhGASA14 regulates the flowering time of upland cotton in response to GA3

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