Genome-wide comparative analyses of GATA transcription factors among 19 Arabidopsis ecotype genomes: Intraspecific characteristics of GATA transcription factors

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. Due to the low cost of genome sequencing, multiple strains of specific species have been sequenced: e.g., number of plant genomes in the Plant Genome Database (http://www.plantgenome.info/) is 2,174 originated from 713 plant species. Thus, we investigated GATA TFs of 19 Arabidopsis thaliana genome-widely to understand intraspecific features of Arabidopsis GATA TFs with the pipeline of GATA database (http://gata.genefamily.info/). Numbers of GATA genes and GATA TFs of each A. thaliana genome range from 29 to 30 and from 39 to 42, respectively. Four cases of different pattern of alternative splicing forms of GATA genes among 19 A. thaliana genomes are identified. 22 of 2,195 amino acids (1.002%) from the alignment of GATA domain amino acid sequences display variations across 19 ecotype genomes. In addition, maximally four different amino acid sequences per each GATA domain identified in this study indicate that these position-specific amino acid variations may invoke intraspecific functional variations. Among 15 functionally characterized GATA genes, only five GATA genes display variations of amino acids across ecotypes of A. thaliana, implying variations of their biological roles across natural isolates of A. thaliana. PCA results from 28 characteristics of GATA genes display the four groups, same to those defined by the number of GATA genes. Topologies of bootstrapped phylogenetic trees of Arabidopsis chloroplasts and common GATA genes are mostly incongruent. Moreover, no relationship between geographical distribution and their phylogenetic relationships was found. Our results present that intraspecific variations of GATA TFs in A. thaliana are conserved and evolutionarily neutral along with 19 ecotypes, which is congruent to the fact that GATA TFs are one of the main regulators for controlling essential mechanisms, such as seed germination and hypocotyl elongation.

Genome-wide comparative analyses of GATA transcription factors among seven Populus genomes

“…In total, 23 out of 556 (4.14%) amino acid positions in the CX 2-4 CX 18-20 CX 2 C region (inter-species variations) show more than one amino acid (Fig. 3 d), which is larger than that of 19 A. thaliana genomes 43 (intraspecific variations; 0.93%). Positions of variable amino acids in the CX 2-4 CX 18-20 CX 2 C region are scattered throughout this region along with PCs (Fig.…”

“…We identified 262 GATA genes (389 GATA TFs) from seven Populus genomes available in public using the pipeline of the GATA-TFDB ( http://gata.genefamily.info/ ; Table S2 ). The number of GATA genes for each Populus genome ranges from 33 to 40 (Table 1 ), which is larger than those of A. thaliana (29 to 30 GATA genes) 25 , 43 , V. vinifera (19 GATA genes), and O. sativa (28 GATA genes) 81 ; while is smaller than that of G. max (64 GATA genes) 40 . The phylogenetic relationship of the seven Populus species inferred from the complete chloroplast genomes (Fig.…”

“…With the published plant genomes, various genome-wide analyses of TF families have been conducted; AP2/ERF, NAC 28 – 31 , bHLH 32 – 34 , bZIP 23 , 35 – 37 , GRAS 20 , 38 , 39 , and GATA 25 , 40 , 41 TF families displaying their features in various aspects including evolutionary aspect. Genome-wide analyses of TF families in Arabidopsis thaliana have also been studied, presenting 122 AP2/ERF genes 42 , 105 NAC genes 28 , 162 bHLH genes 34 , 75 bZIP genes 23 , 32 GRAS genes 20 , 29 GATA genes 25 as well as 566 GATA genes from 19 A. thaliana genomes 43 .…”

“…Most plant GATA TFs contain a single GATA domain of which pattern is CX 2 CX 18 CX 2 C (type IV b ) or CX 2 CX 20 CX 2 C (type IV c ) 27 . Except for these known types, additional patterns were also identified: e.g., CX 4 CX 18 CX 2 X, which have four amino acids in the first Cysteine-Cysteine, named as type IV 4 43 .…”

“…Plant GATA TFs have various roles like the chloroplast development 46 , photosynthesis and growth 47 , epithelial innate immune responses 48 , seed germination 49 , hypocotyl and petiole elongation 50 , and cryptochrome1-dependent response 51 . Genome-wide analyses and/or expression analyses of GATA TFs have been reported in 21 plant species 25 , 40 , 41 , 43 , 52 – 66 (Table S1 ), including P. trichocarpa of which genome-wide identification of GATA genes was conducted based on the old gene model (Version 3.0; Table S1 ).…”