Genome-wide identification and analysis of the evolution and expression patterns of the GATA transcription factors in three species of Gossypium genus

Zhang, Zhen; Zou, Xianyan; Huang, Zhen; Fan, Senmiao; Gě, Qún; Liú, Àiyīng; Gōng, Jǔwǔ; Lǐ, Jùnwén; Gǒng, Wànkuí; Shí, Yùzhēn; Fan, Liqiang; Zhang, Zhibin; Liu, Ruixian; Jiang, Xiao; Lei, Kang; Shāng, Hǎihóng; Xu, Aidong; Yuán, Yǒulù

doi:10.1016/j.gene.2018.09.039

Cited by 34 publications

(43 citation statements)

References 65 publications

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“…We also found upregulation of 12 GATA genes which indicates that they play an important role in embryo initiation in cotton. GATA TFs are widely distributed in fungi, animals, and plants consist of a protein family containing a DNA-binding domain recognizing the DNA consensus sequence (A/T) GATA(A/G) and one or two highly conserved type-IV zinc ngers (C-X2-C-X17 − 20-C-X2-C) [64]. In plants, GATA TF expression is involved in light-mediated processes such as owering, maturation, petal differentiation and expansion, and embryo development.…”

Section: Discussionmentioning

confidence: 99%

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Transcriptomic profiles of non-embryogenic and embryogenic callus cells in a highly regenerative Upland Cotton line (Gossypium hirsutum L.)

Parris

et al. 2020

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• Background • Genotype independent transformation and whole plant regeneration through somatic embryogenesis relies heavily on the intrinsic ability of a genotype to regenerate. • Results • In this study, gene expression profiles of a highly regenerable Gossypium hirsutum L. cultivar, Jin668, were analyzed at two critical developmental stages during somatic embryogenesis, non-embryogenic callus (NEC) cells and embryogenic callus (EC) cells. The rate of EC formation in Jin668 is 96%. Differential gene expression analysis revealed a total of 5,333 differentially expressed genes (DEG) with 2,534 upregulated and 2,799 downregulated in EC. A total of 144 genes were unique to NEC cells and 174 genes unique to EC. Clustering and enrichment analysis identified genes upregulated in EC that function as transcription factors/DNA binding, phytohormone response, oxidative reduction, and regulators of transcription; while genes categorized in methylation pathways were downregulated. Four key transcription factors were identified based on their sharp upregulation in EC tissue; LEAFY COTYLEDON 1 (LEC1), BABY BOOM (BBM), FUSCA (FUS3) and AGAMOUS-LIKE15 with distinguishable subgenome expression bias. • Conclusions • This comparative analysis of NEC and EC transcriptomes gives new insights into the genetic underpinnings of somatic embryogenesis in cotton.

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Section: Discussionmentioning

confidence: 99%

“…[65]. In the Gossypium genus, 30 GATA TFs have been identi ed [64]. Moreover, Nawy et al reported that a GATA transcription factor, HANABA TARANU (HAN) was required to position the inductive Arabidopsis pro-embryo boundary and revealed that HAN regulated transcription in the basal pro-embryo [66].…”

Section: Discussionmentioning

confidence: 99%

Transcriptomic profiles of non-embryogenic and embryogenic callus cells in a highly regenerative Upland Cotton line (Gossypium hirsutum L.)

Parris

et al. 2020

Preprint

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“…We con rmed chromosomal locations of the OMT family genes in Gossypium as previously described (Zhang et al 2019). A total of 161 OMT genes were positioned on their respective chromosomes, while seven of G. raimondii, one of G. arboreum, and 23 of G. hirsutum were positioned in scaffolds (S4 Figure).…”

Section: Chromosomal Distribution Collinearity Duplication and Losmentioning

confidence: 95%

Biodiverse Responses of O-methyltransferase Genes to Salt Stress and Fiber Development of Gossypium Species

Hafeez

Gě

Zhāng

et al. 2020

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O-methyltransferases (OMTs) are an important group of enzymes that catalyze the transfer of a methyl group from S-adenosyl-L-methionine to their acceptor substrates. OMTs are divided into several groups according to their structural features. In Gossypium species, they are involved in phenolics and flavonoid pathways. Phenolics defend the cellulose fiber from dreadful external conditions of biotic and abiotic stresses, promoting strength and growth of plant cell wall. In this study, an OMT gene family, containing a total of 192 members, has been identified and characterized in three main Gossypium species, G. hirsutum, G. arboreum and G. raimondii. Cis-regulatory elements analysis suggested important roles of OMT genes in growth, development, and defense against stresses. Transcriptome data of different fiber developmental stages in Chromosome Substitution Segment Lines (CSSLs), Recombination Inbred Lines (RILs) with excellent fiber quality, and standard genetic cotton cultivar TM-1 demonstrate that up-regulation of OMT genes at different fiber developmental stages, and abiotic stress treatments have some significant correlations with fiber quality formation, and with salt stress response. Quantitative RT-PCR results revealed that GhOMT43 and GhOMT27 genes had a specific expression in response to salt stress while GhOMT16, GhOMT55, and GhOMT33 in fiber elongation and secondary cell wall stages. Our results indicated that these genes might contribute to salt tolerance or fiber quality traits respectively in Gossypium.

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“…The GATA member PdGNC in Populus plays a crucial role in photosynthesis and plant growth (An et al, 2019). In wheat, overexpression of TaZIM-A1, a member of the GATA family, caused the delay of owering and the decrease of thousand-kernel weight (Liu et al, 2018).…”

Section: Introductionmentioning

confidence: 99%

Genome-Wide Identification and Characterization of GATA Family Genes in Brassica Napus

Zhu

Guo

Chen

et al. 2020

Preprint

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Background: GATA transcription factors are involved in plant developmental processes, which also respond to environmental stresses through binding DNA regulatory regions to regulate the downstream genes. However, little information of GATA genes is available in Brassica napus, one of important oil crops. The release of B. napus genome sequences provides a good opportunity to perform a genome-wide characterization of GATA family genes in the rapeseed genome. Results: In this study, 96 GATA genes randomly distributing on 19 chromosomes were identified in B. napus. They were classified into four subfamilies on the basis of phylogenetic analysis and the domain structures. The sequences of BnGATAs were obvious divergence among four subfamilies based on their GATA domains, structures and motif compositions. Gene duplication and the synteny between the genomes of B. napus and A. thaliana were also analyzed to provide insights into the evolutionary characteristics. Moreover, BnGATAs showed different expression patterns in various tissues and under diverse abiotic stresses. Single nucleotide polymorphisms (SNPs) distribution analysis suggests functional disparity of GATA family genes in different genotypes of a core collection germplasm.Conclusion: This study examined genomic structures, evolution features, expression patterns and SNP distribution of 96 BnGATAs. The results enriched our knowledge of the GATA genes in rapeseed.

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Genome-wide identification and analysis of the evolution and expression patterns of the GATA transcription factors in three species of Gossypium genus

Cited by 34 publications

References 65 publications

Transcriptomic profiles of non-embryogenic and embryogenic callus cells in a highly regenerative Upland Cotton line (Gossypium hirsutum L.)

Transcriptomic profiles of non-embryogenic and embryogenic callus cells in a highly regenerative Upland Cotton line (Gossypium hirsutum L.)

Biodiverse Responses of O-methyltransferase Genes to Salt Stress and Fiber Development of Gossypium Species

Genome-Wide Identification and Characterization of GATA Family Genes in Brassica Napus

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