Abstract
The Dof domain protein family is a classic plant-specific zinc-finger transcription factor family involved in a variety of biological processes. There is great diversity in the number of Dof genes in different plants. However, there are only very limited reports on the characterization of Dof transcription factors in soybean (Glycine max). In the present study, 78 putative Dof genes were identified from the whole-genome sequence of soybean. The predicted GmDof genes were non-randomly distributed within and across 19 out of 20 chromosomes and 97.4% (38 pairs) were preferentially retained duplicate paralogous genes located in duplicated regions of the genome. Soybean-specific segmental duplications contributed significantly to the expansion of the soybean Dof gene family. These Dof proteins were phylogenetically clustered into nine distinct subgroups among which the gene structure and motif compositions were considerably conserved. Comparative phylogenetic analysis of these Dof proteins revealed four major groups, similar to those reported for Arabidopsis and rice. Most of the GmDofs showed specific expression patterns based on RNA-seq data analyses. The expression patterns of some duplicate genes were partially redundant while others showed functional diversity, suggesting the occurrence of sub-functionalization during subsequent evolution. Comprehensive expression profile analysis also provided insights into the soybean-specific functional divergence among members of the Dof gene family. Cis-regulatory element analysis of these GmDof genes suggested diverse functions associated with different processes. Taken together, our results provide useful information for the functional characterization of soybean Dof genes by combining phylogenetic analysis with global gene-expression profiling.
Highlights
The transcriptional regulation of gene expression influences or controls many important cellular processes, such as signal transduction, morphogenesis, and environmental stress responses [1]
A total of 79 non-redundant Dof transcription factor-encoding genes were identified from the whole genome
The presence of the conserved Dof domain in the predicted GmDof protein was a typical feature for consideration as a member of the Dof Transcription factors (TFs) family
Summary
The transcriptional regulation of gene expression influences or controls many important cellular processes, such as signal transduction, morphogenesis, and environmental stress responses [1]. Transcription factors (TFs) are a group of proteins that control cellular processes by regulating the expression of downstream target genes [2]. The identification and functional characterization of TFs is essential for the reconstruction of transcriptional regulatory networks [3]. In plants, ~60 families of TFs have been identified based on bioinformatics analysis and manual inspection [4,5]. The Arabidopsis genome codes for at least 1533 TFs, which account for about 5.9% of its estimated total number of genes [1]. As for soybean (Glycine max), ~12.2% of the 46,430 predicted protein-coding loci have been identified to encode 5,671 putative TFs [6]
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