Identification and expression analysis of the DREB transcription factor family in pineapple (Ananas comosus (L.) Merr.)

Abstract

Background: Dehydration responsive element-binding (DREB) transcription factors play a crucial role in plant growth, development and stress responses. Although DREB genes have been characterized in many plant species, genome-wide identification of the DREB gene family has not yet been reported in pineapple (Ananas comosus (L.) Merr.).

Results: Using comprehensive genome-wide screening, we identified 20 AcoDREB genes on 14 chromosomes. These were categorized into five subgroups. AcoDREBs within a group had similar gene structures and domain compositions. Using gene structure analysis, we showed that most AcoDREB genes (75%) lacked introns, and that the promoter regions of all 20 AcoDREB genes had at least one stress response-related cis-element. We identified four genes with high expression levels and six genes with low expression levels in all analyzed tissues. We detected expression changes under abiotic stress for eight selected AcoDREB genes.

Conclusions: This report presents the first genome-wide analysis of the DREB transcription factor family in pineapple. Our results provide preliminary data for future functional analysis of AcoDREB genes in pineapple, and useful information for developing new pineapple varieties with key agronomic traits such as stress tolerance.

Keywords: DREB transcription factors; Expression profiles; Phylogenetic analysis; Pineapple.

Figure 1. Locations of AcoDREB genes on the pineapple chromosomes.

(A–G) Different chromosomes. The chromosome number is indicated above each bar and the length of the bar represents the size of the chromosome in pineapple. Gene star point is shown on chromosome. The figure was generated using MapChart.

Figure 2. Multiple sequence alignment of the AP2 domain of AcoDREB proteins.

The alignment was performed using the DNAMAN. Conserved V14, E19, YRG and RAYD motifs are highlighted by the asterisks and lines.

Figure 3. Phylogenetic analysis of DREB proteins in pineapple (Aco), Arabidopsisand rice.

The proteins are classified into five groups: I, II, III, IV and Ⅴ. Classification of Arabidopsis by Sakuma et al. (2002) is indicated in parentheses. Different individual subfamilies were shown by different colors.

Figure 4. Predicted cis-elements in AcoDREB promoter regions.

Promoter sequences (−2000 bp) of 20 AcoDREB were analyzed by PlantCARE. The upstream length to the translation start site can be inferred according to the scale.

Figure 5. Exon–intron organization of AcoDREB genes.

Black bars indicates exon (CDS), Gray bars indicated UTR while plain lines showing introns.

Figure 6. The conserved motifs of the predicted AcoDREB proteins.

The conserved motifs in the AcoDREB proteins were identified with MEME software. Grey lines denote the non-conserved sequences, and each motif is indicated by a colored box. The length of motifs in each protein was presented proportionally.

Figure 7. Heatmap showing the expression levels of AcoDREB genes in different pineapple tissues.

RNA-Seq expression level can be understood using the givenscale and roman numbers on right-side shows clusters based on gene expression. O, S and G represent ovule, stamen and gynoecium, respectively.

Figure 8. The expression profiles of AcoDREB genes in nine tissues validated by qRT-PCR.

Validation of 16 genes at nine different tissues through qRT-PCR. Heat-map was constructed from relative gene expression in different tissues (qRT-PCR) data.

Figure 9. qRT-PCR expression analysis of eight selected AcoDREB genes in response to different abiotic stress treatments.

(A)–(H) High salt (150 mM NaCl); (I)–(P) drought (350 Mm Mannitol); (Q)–(X) chilling, exposure to 4 °C; (Y)–(FF) high temperature, exposure to 45 °C. Mean expression value was calculated from three independent replicates. Error bars indicate the standard deviation. Data are presented as mean ± standard deviation (SD). Asterisks on top of the bars indicating statistically significant differences between the stress and counterpart controls (*P < 0.05, **P < 0.01).