Identification of Dof transcription factors in Dendrobium huoshanense and expression pattern under abiotic stresses

Abstract

Introduction: DNA-binding with one finger (Dof) transcription factors (TFs) are a unique family of TFs found in higher plants that regulate plant responses to light, hormones, and abiotic stresses. The specific involvement of Dof genes in the response to environmental stresses remains unknown in D. huoshanense. Methods: A total of 22 Dof family genes were identified from the D. huoshanense genome. Results: Chromosome location analysis showed that DhDof genes were distributed on 12 chromosomes, with the largest number of Dof genes located on chromosome 8. The phylogenetic tree revealed that DhDofs could be categorized into 11 distinct subgroups. In addition to the common groups, DhDof4, DhDof5, DhDof17, and the AtDof1.4 ortholog were clustered into the B3 subgroup. Group E was a newly identified branch, among which DhDof6, DhDof7, DhDof8, and DhDof9 were in an independent branch. The conserved motifs and gene structure revealed the differences in motif number and composition of DhDofs. The dof domain near the N-terminus was highly conserved and contained a C₂-C₂-type zinc finger structure linked with four cysteines. Microsynteny and interspecies collinearity revealed gene duplication events and phylogenetic tree among DhDofs. Large-scale gene duplication had not occurred among the DhDofs genes and only in one pair of genes on chromosome 13. Synteny blocks were found more often between D. huoshanense and its relatives and less often between Oryza sativa and Arabidopsis thaliana. Selection pressure analysis indicated that DhDof genes were subject to purifying selection. Expression profiles and correlation analyses revealed that the Dof gene under hormone treatments showed several different expression patterns. DhDof20 and DhDof21 had the highest expression levels and were co-expressed under MeJA induction. The cis-acting element analysis revealed that each DhDof had several regulatory elements involved in plant growth as well as abiotic stresses. qRT-PCR analysis demonstrated that DhDof2 was the main ABA-responsive gene and DhDof7 was the main cold stress-related gene. IAA suppressed the expression of some Dof candidates, and SA inhibited most of the candidate genes. Discussion: Our results may provide new insights for the further investigation of the Dof genes and the screening of the core stress-resistance genes.

Keywords: DNA binding with one finger; Dendrobium huoshanense; abiotic stress; bioinformactics analysis; phylogeny.

FIGURE 1

Chromosomal location analysis of the DhDof genes.

FIGURE 2

Phylogenetic tree of Dof proteins from D. huoshanense and A. thaliana. (A) Neighbor-joining method; (B) Maximum-likelihood method.

FIGURE 3

Conserved motif and exon/intron analysis of the DhDof gene. (A) Conserved motif; (B) conserved domain; (C) cds, introns and UTR.

FIGURE 4

Multiple sequence alignments of the Dof protein. “C” stands for cysteine. The dashed line represents the zinc-finger motif of the Dof domain.

FIGURE 5

Comparative genomic analysis of Dof genes. (A) Microsynteny of DhDof genes; (B) Collinearity of D. huoshanense with D. nobile, D. chrysotoxum, O. sativa and A. thaliana. The ticks and scatter points are the genome scale and gene density, respectively. Gray lines represent shared gene pairs.

FIGURE 6

Expression profile and correlation analysis of the DhDof gene. (A) Expression profile after MeJA treatment; (B) correlation analysis of DhDof genes. Mean_Control, Mean_T1, Mean_T2, Mean_T3, Mean_T4, Mean_T5, Mean_T6, and Mean_T7 represent the groups treated with MeJA after 0, 0.25, 0.5, 1.0, 2.0, 4.0, 8.0, and 16.0 h, respectively.

FIGURE 7

Analysis of cis-acting elements of the DhDof gene. (A) Distribution and composition of elements on the promoter of the DhDof gene; (B) Number and proportion of elements in the DhDof gene; (C) Functional classification and proportion of the DhDof gene.

FIGURE 8

qRT-PCR analysis of the DhDof gene. (A) ABA treatment; (B) GA treatment; (C) IAA treatment; (D) MeJA treatment; (E) SA treatment; (F) low temperature treatment.