Genome-wide analysis of the Dof transcription factor gene family reveals soybean-specific duplicable and functional characteristics
Authors: Li-Juan Qiu
Yong Guo
Journal: PLoS ONE (2013)
Discipline: Multidisciplinary
Keywords: Dof domain protein; zinc-finger transcription factor; soybean; gene duplication; phylogenetic analysis
Affiliations: The National Key Facility for Crop Gene Resources and Genetic Improvement (NFCRI)/Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, P. R. China.

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. 

Retracted: Yes

PubPeer comments:
 The authors acknowledge that there are overlaps between the text of this article and the following previously published work, which was not cited: Hu R, Guang Q, Yingzhen K, Dejing K, Gao Q and Zhou G (2010) Comprehensive Analysis of NAC Domain Transcription Factor Gene Family in Populus trichocarpa. BMC Plant Biology. DOI: 10.1186 1471-2229-10-14 The authors apologize for the overlap in text. The PLOS ONE Editors have also identified overlaps between the text of this article and a number of previously published works. Text was duplicated verbatim or with minor modifications from the sources listed below: Genome wide identification of Dof transcription factor gene family in sorghum and its comparative phylogenetic analysis with rice and Arabidopsis. Molecular Biology Reports. DOI: 10.1007 s11033-010-0650-9 (cited as Reference 11 in the published article) Dof Domain Proteins: Plant-Specific Transcription Factors Associated with Diverse Phenomena Unique to Plants. Plant Cell Physiology. DOI: 10.1093 pcp pch055 (cited as Reference 14 in the published article) Genome-wide Analysis of Plant-specific Dof Transcription Factor Family in Tomato. Journal of Integrative Plant Biology. DOI: 10.1111 jipb.12043 (cited as Reference 57 in the published article) Identification of cis-regulatory elements specific for different types of reactive oxygen species in Arabidopsis thaliana. Gene. DOI: 10.1016 j.gene.2012.02.035 (uncited in the published article) The family of DOF transcription factors in Brachypodium distachyon: phylogenetic comparison with rice and barley DOFs and expression profiling. BMC Plant Biology. DOI: 10.1186 1471-2229-12-202 (cited as Reference 54 in the published article) In light of the concerns identified, the authors and the PLOS ONE Editors retract this article. 17 Nov 2016: Guo Y, Qiu LJ, PLOS ONE Editors (2016) Retraction: Genome-Wide Analysis of the Dof Transcription Factor Gene Family Reveals Soybean-Specific Duplicable and Functional Characteristics. PLOS ONE 11(11): e0167019. https: doi.org 10.1371 journal.pone.0167019 View retraction ,