Abstract
GATA transcription factors (TFs) are widespread eukaryotic regulators whose DNA-binding domain is a class IV zinc finger motif (CX2CX17–20CX2C) followed by a basic region. We identified 262 GATA genes (389 GATA TFs) from seven Populus genomes using the pipeline of GATA-TFDB. Alternative splicing forms of Populus GATA genes exhibit dynamics of GATA gene structures including partial or full loss of GATA domain and additional domains. Subfamily III of Populus GATA genes display lack CCT and/or TIFY domains. 21 Populus GATA gene clusters (PCs) were defined in the phylogenetic tree of GATA domains, suggesting the possibility of subfunctionalization and neofunctionalization. Expression analysis of Populus GATA genes identified the five PCs displaying tissue-specific expression, providing the clues of their biological functions. Amino acid patterns of Populus GATA motifs display well conserved manner of Populus GATA genes. The five Populus GATA genes were predicted as membrane-bound GATA TFs. Biased chromosomal distributions of GATA genes of three Populus species. Our comparative analysis approaches of the Populus GATA genes will be a cornerstone to understand various plant TF characteristics including evolutionary insights.
Highlights
GATA transcription factors (TFs) are widespread eukaryotic regulators whose DNA-binding domain is a class IV zinc finger motif (CX2CX17–20CX2C) followed by a basic region
We identified that some alternative splicing forms of the twelve GATA genes of three Populus species (P. tremula x alba, P. tremula, and P. tremuloides; Table S5) missed GATA domain which was not included in the Populus GATA TFs list
Using the identification pipeline of GATA TFs in the GATA-TFDB, we successfully identified 262 GATA genes (389 GATA TFs) from seven Populus species
Summary
GATA transcription factors (TFs) are widespread eukaryotic regulators whose DNA-binding domain is a class IV zinc finger motif (CX2CX17–20CX2C) followed by a basic region. GATA TFs contain more than one highly conserved type IV zinc finger motifs ( CX2X17–20CX2C) followed by a basic region that can bind to a consensus DNA sequence, WGATAR(W means T or A; R indicates G or A)[25, 44, 45]. Most plant GATA TFs contain a single GATA domain of which pattern is C X2CX18CX2C (type IVb) or CX2CX20CX2C (type I Vc)[27] Except for these known types, additional patterns were identified: e.g., CX4CX18CX2X, which have four amino acids in the first Cysteine-Cysteine, named as type I V443. In spite of abundant resources of Salicaceae genomes including Salix purpurea[79], there is only one study for characterizing the biological function of Populus GATA gene (PdGNC), which regulates chloroplast ultrastructure, photosynthesis, and vegetative growth in Arabidopsis[80], suggesting genome-wide identification of Populus GATA genes are strongly required
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