Abstract
Transcription factors (TFs) form the major class of regulatory genes and play key roles in multiple plant stress responses. In most eukaryotic plants, transcription factor (TF) families (WRKY, MADS-box and MYB) activate unique cellular-level abiotic and biotic stress-responsive strategies, which are considered as key determinants for defense and developmental processes. Arabidopsis and rice are two important representative model systems for dicot and monocot plants, respectively. A comprehensive comparative study on 101 OsWRKY, 34 OsMADS box and 122 OsMYB genes (rice genome) and, 71 AtWRKY, 66 AtMADS box and 144 AtMYB genes (Arabidopsis genome) showed various relationships among TFs across species. The phylogenetic analysis clustered WRKY, MADS-box and MYB TF family members into 10, 7 and 14 clades, respectively. All clades in WRKY and MYB TF families and almost half of the total number of clades in the MADS-box TF family are shared between both species. Chromosomal and gene structure analysis showed that the Arabidopsis-rice orthologous TF gene pairs were unevenly localized within their chromosomes whilst the distribution of exon–intron gene structure and motif conservation indicated plausible functional similarity in both species. The abiotic and biotic stress-responsive cis-regulatory element type and distribution patterns in the promoter regions of Arabidopsis and rice WRKY, MADS-box and MYB orthologous gene pairs provide better knowledge on their role as conserved regulators in both species. Co-expression network analysis showed the correlation between WRKY, MADs-box and MYB genes in each independent rice and Arabidopsis network indicating their role in stress responsiveness and developmental processes.
Highlights
Transcription factors (TFs) are characterized as proteins with at least one domain that corresponds to a specificDNA binding site and control the transcriptional regulatory schemes in plant cells
OsWRKY, 34 OsMADS box and 122 OsMYB sequences were identified in rice and 72 AtWRKY, 66 AtMADS box and 144 AtMYB sequences were identified in Arabidopsis after the repetitive and redundant gene sequences were removed
A phylogenetic tree for the WRKY transcription factor (TF) family was built from 173 collated Arabidopsis and rice WRKY genes
Summary
Transcription factors (TFs) are characterized as proteins with at least one domain that corresponds to a specificDNA binding site and control the transcriptional regulatory schemes in plant cells. 58 different TF families are deposited in the PlantTFDB database and they have been exclusively characterized in model plants[3] Amongst these TF families, WRKY, MADS-box and MYB are the most important transcriptional regulators that are widely distributed in the plant kingdom and actively involved in plant development and, biotic and abiotic stress r esponses[4]. The TFs with MCM1/AGAMOUS/DEFICIENS/SRF (MADS)-box regulate the developmental processes such as seed germination, vegetative growth, the transition from vegetative to reproductive growth, floral development and senescence and regulating the abiotic and biotic stress tolerance They contain a conserved MADS domain consists of 60-amino acid long at the N-terminal and recognizes the CArG-box DNA motif (CC[A/]6GG) in the target genes. The MADS-box TF family contains more than 100 members and are generally involved in almost every developmental process of a higher p lant[22]
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