Plant GATA transcription factors (TFs) constitute a conserved family of zinc finger proteins characterized by a type IV zinc finger motif (CX2CX18-20CX2C) that binds to the WGATAR (W = A/T, R = A/G). Given their essential roles in plant growth, development, and environmental adaptation, GATA TFs have been extensively investigated through genome-wide analyses across diverse plant species. However, despite its economic importance as a major root crop, the carrot (Daucus carota subsp. sativus) has not yet undergone a comprehensive genome-wide analysis of its GATA TF family. To address this gap, this study conducted a comprehensive in-silico characterization of the GATA TF family in the carrot genome. A total of 33 DcGATAs were classified into four classes, with Classes A and B containing relatively more members than Classes C and D. Each class displayed distinct conserved gene, domain, and motif structures. Chromosome distribution and collinearity analysis revealed that the 33 DcGATAs were unevenly distributed across the nine carrot chromosomes and formed 16 intergroup syntenic gene pairs, indicating that segmental duplication may have contributed to the expansion of the gene family. Secondary and tertiary structure analyses indicated that DcGATA genes were mainly enriched in random coils with lower proportions of α-helices, extended strands, and β-turns. Protein–protein interaction analysis suggested a broad interaction network among DcGATA genes at low confidence, with only a limited number of interactions detected at medium confidence. Cis-acting element analysis revealed 1,106 regulatory elements in DcGATA promoters, predominantly associated with light, stress, and hormone responses, with class-specific variation in element abundance. RNA-seq expression profiling showed that only a subset of DcGATA genes exhibited significant variation across developmental stages, root colors, and their interactions, whereas most genes maintained stable expression in 40- and 80-DAP yellow and orange roots. MiRNA target prediction revealed 45 miRNAs targeting 15 DcGATA genes, mainly involving MIR159, MIR165, and MIR396 families, with class-specific cleavage- and translation-mediated regulatory patterns. These results provide comprehensive insights into the evolution and functional diversification of DcGATAs by establishing an in-silico integrative regulatory framework; however, further experimental validation is required to elucidate their precise roles in development and stress adaptation.

Genome-wide in-silico characterization and expression pattern analysis of GATA transcription factor family in carrot (Daucus carota subsp. sativus)

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发表日期：

2026年7月8日

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Mangi Kim

摘要

Plant GATA transcription factors (TFs) constitute a conserved family of zinc finger proteins characterized by a type IV zinc finger motif (CX₂CX_18-20CX₂C) that binds to the WGATAR (W = A/T, R = A/G). Given their essential roles in plant growth, development, and environmental adaptation, GATA TFs have been extensively investigated through genome-wide analyses across diverse plant species. However, despite its economic importance as a major root crop, the carrot (Daucus carota subsp. sativus) has not yet undergone a comprehensive genome-wide analysis of its GATA TF family. To address this gap, this study conducted a comprehensive in-silico characterization of the GATA TF family in the carrot genome. A total of 33 DcGATAs were classified into four classes, with Classes A and B containing relatively more members than Classes C and D. Each class displayed distinct conserved gene, domain, and motif structures. Chromosome distribution and collinearity analysis revealed that the 33 DcGATAs were unevenly distributed across the nine carrot chromosomes and formed 16 intergroup syntenic gene pairs, indicating that segmental duplication may have contributed to the expansion of the gene family. Secondary and tertiary structure analyses indicated that DcGATA genes were mainly enriched in random coils with lower proportions of α-helices, extended strands, and β-turns. Protein–protein interaction analysis suggested a broad interaction network among DcGATA genes at low confidence, with only a limited number of interactions detected at medium confidence. Cis-acting element analysis revealed 1,106 regulatory elements in DcGATA promoters, predominantly associated with light, stress, and hormone responses, with class-specific variation in element abundance. RNA-seq expression profiling showed that only a subset of DcGATA genes exhibited significant variation across developmental stages, root colors, and their interactions, whereas most genes maintained stable expression in 40- and 80-DAP yellow and orange roots. MiRNA target prediction revealed 45 miRNAs targeting 15 DcGATA genes, mainly involving MIR159, MIR165, and MIR396 families, with class-specific cleavage- and translation-mediated regulatory patterns. These results provide comprehensive insights into the evolution and functional diversification of DcGATAs by establishing an in-silico integrative regulatory framework; however, further experimental validation is required to elucidate their precise roles in development and stress adaptation.