Genome-Wide Characterization, Evolution, and Expression Profiling of VQ Gene Family in Response to Phytohormone Treatments and Abiotic Stress in Eucalyptus grandis

Abstract

VQ genes play important roles in plant development, growth, and stress responses. However, little information regarding the functions of VQ genes is available for Eucalyptus grandis. In our study, genome-wide characterization and identification of VQ genes were performed in E. grandis. Results showed that 27 VQ genes, which divided into seven sub-families (I-VII), were found, and all but two VQ genes showed no intron by gene structure and conserved motif analysis. To further identify the function of EgrVQ proteins, gene expression analyses were also developed under hormone treatments (brassinosteroids, methyl jasmonate, salicylic acid, and abscisic acid) and abiotic conditions (salt stress, cold 4 °C, and heat 42 °C). The results of a quantitative real-time PCR analysis indicated that the EgrVQs were variously expressed under different hormone treatments and abiotic stressors. Our study provides a comprehensive overview of VQ genes in E. grandis, which will be beneficial in the molecular breeding of E. grandis to promote its resistance to abiotic stressors; the results also provide a basis from which to conduct further investigation into the functions of VQ genes in E. grandis.

Keywords: Eucalyptus grandis; VQ genes family; abiotic stress; expression pattern; plant hormones.

Figure 1

Chromosomal location of E. grandis VQ genes. Chromosome numbers were indicated above each chromosome. The size of a chromosome was indicated by its relative length. Gene positions and chromosome sizes were given in megabases (Mb) to the left of the figure. Tandem duplicated genes were underlined in red.

Figure 2

Phylogenetic tree of VQ proteins from E. grandis, Arabidopsis, rice, and poplar. ClustalW softwarealigned the complete amino acid sequences of 27 E. grandis (prefixed with ‘Egr’), 34 Arabidopsis (prefixed with ‘At’), 40 rice (prefixed with ‘Os’), and 51 (prefixed with ‘Pt’) VQ proteins, and MEGA 7, with 1000 bootstrap replicates, constructed the neighbor-joining tree.

Figure 3

Multiple sequence alignment of VQ proteins in E. grandis. Sequences were aligned using DNAMAN software. The FxxxVQxxxG motif was highly conserved. The dark blue indicated the conserved section of EgrVQs protein family. The pink indicated the four conserved motif variations of LGT, FTG, VTG, and LSG.

Figure 4

Gene structure of VQ genes in E. grandis. Exons were indicated by yellow rectangles. Upstream/downstream’s sequences of EgrVQs were indicated by blue lines. Gray lines connecting two exons represented introns.

Figure 5

Phylogenetic relationships and conserved motifs of VQ proteins in E. grandis. The left panel showed the phylogenetic tree of EgrVQ, which was constructed by the neighbor-joining method based on the results of sequence alignment. Proteins were divided into seven subgroups (marked by different colors). The right panel showed the distribution of the 20 conserved motifs in the EgrVQ genes following analysis with Multiple Expectation Maximization for Motif Elicitation (MEME). Each specific motif was marked by a different colored box, and the motif numbers were included in the center of each box. The length of each box was proportional to the actual size of the motif.

Figure 6

Semi-quantitative Real-Time PCR (RT-PCR) of the expression of EgrVQ genes in different tissues. From left to right: root, xylem, phloem, mature leaves, and young leaves. All of these tissues were collected from 6-week-old GL1 plants.

Figure 7

Expression analysis of 25 EgrVQ genes in E. grandis following brassinosteroid (BR) (A), salicylic acid (SA) (B), methyl jasmonate (MeJA) (C), and abscisic acid (ABA) (D) treatment, as determined by Real-Time quantitative PCR (qRT-PCR). The relative expression levels were calculated using the 2^−ΔΔCt method. The heatmap was created using MEV.

Figure 8

Expression analysis of 25 EgrVQ genes in E. grandis following cold (A), heat (B), and NaCl (C) treatments, as determined by qRT-PCR. The relative expression levels were calculated using the 2^−ΔΔCt method. The heatmap was created using MEV.