Elsevier

Gene

Volume 687, 1 March 2019, Pages 298-307
Gene

Research paper
Genome-wide identification and characterization of the Dof gene family in cassava (Manihot esculenta)

https://doi.org/10.1016/j.gene.2018.11.053Get rights and content
Under a Creative Commons license
open access

Highlights

  • The first genome-wide identification of Dof family genes was performed in cassava, resulting in a relatively high number of 45 members.

  • These MeDof genes are unevenly distributed across 17 out of the 18 chromosomes.

  • A high number of MeDof duplicates (21) were identified.

  • The majority of MeDof paralogs were derived from the recent whole-genome duplication and only one from local duplication.

  • Comparison of conserved motifs and expression profiles revealed divergence of MeDof duplicates.

Abstract

Dof proteins comprise a plant-specific transcription factor family involved in regulation of many plant processes. Despite their diverse roles, little information is available in cassava (Manihot esculenta, Euphorbiaceae), the sixth major staple crop in the world. This study presents the first genome-wide identification of Dof family genes in cassava, resulting in 45 family members that are unevenly distributed across 17 out of the 18 chromosomes. Phylogenetic analysis assigned these genes into eight groups representing four subfamilies. Synteny analysis and BRH (Best Reciprocal Hit) method were also adopted to study evolutionary relationships. Among 21 MeDof duplicates identified, the majority of them were derived from the recent whole-genome duplication (WGD), whereas only one from local duplication. Transcriptional profiling revealed diverse expression patterns among various tissues, and further comparison of conserved motifs and expression profiles revealed divergence of MeDof duplicates. These findings provide valuable information for functional analysis of Dof genes in cassava.

Abbreviations

Arabidopsis thaliana Dof transcription factor
AtDof
BRH
Best reciprocal hit
CDF
Cycling DOF factor
Chr
Chromosome
Dof
DNA binding with one finger
EST
Expressed sequence tag
FPKM
Fragments per kilobase of exon per million fragments mapped
GRAVY
Grand average of hydropathicity
Ka
nonsynonymous substitution rate
Ks
synonymous substitution rate
Manihot esculenta Dof transcription factor
MeDof
MW
Molecular weight
Mya
Million years ago
NLS
Nuclear localization signal
OBP
OBF binding protein
OBF
ocs element binding factor
Oryza sativa Dof transcription factor
OsDof
pI
Isoelectric point
RNA-seq
RNA sequencing
TCP14
TCP transcription factor 14
WGD
Whole-genome duplication

Keywords

Dof transcription factor
Evolution
Gene expansion
Synteny analysis
Transcriptional profiling
Whole-genome duplication

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