Genome-Wide Identification, Characterization and Expression Profiling of ADF Family Genes in Solanum lycopersicum L

Abstract

The actin depolymerizing factor (ADF) proteins have growth, development, defense-related and growth regulatory functions in plants. The present study used genome-wide analysis to investigate ADF family genes in tomato. Eleven tomato ADF genes were identified and differential expression patterns were found in different organs. SlADF6 was preferentially expressed in roots, suggesting its function in root development. SlADF1, SlADF3 and SlADF10 were predominately expressed in the flowers compared to the other organs and specifically in the stamen compared to other flower parts, indicating their potential roles in pollen development. The comparatively higher expression of SlADF3 and SlADF11 at early fruit developmental stages might implicate them in determining final fruit size. SlADF5 and SlADF8 had relatively higher levels of expression five days after the breaker stage of fruit development, suggesting their possible role in fruit ripening. Notably, six genes were induced by cold and heat, seven by drought, five by NaCl, and four each by abscisic acid (ABA), jasmonic acid (JA) and wounding treatments. The differential expression patterns of the SlADF genes under different types of stresses suggested their function in stress tolerance in tomato plants. Our results will be helpful for the functional characterization of ADF genes during organ and fruit development of tomato under different stresses.

Keywords: ADF gene; Solanum lycopersicum; abiotic stress; fruit development; organ-specific expression; phytohormone treatment.

Figure 1

Schematic representation of the exon-intron distribution in the tomato actin depolymerizing factor (ADF) gene family. The red boxes represent the exons and the green lines represent the introns. Asterisks indicate the ADF-H domain position in the exon. The numbers represent the length of exons and introns in bp.

Figure 2

Alignment of all deduced tomato ADF polypeptides with those of Arabidopsis, rice and cotton. Asterisks indicate the putative serine phosphorylation site. The red box indicates the putative CAM binding site and the green box indicates the amino acid residues essential for actin binding. The dark black background highlights the identical amino acids and the light background highlights the amino acids with >50% identity. The blue underline represents the ADF-H domain position.

Figure 3

Phylogenetic tree of tomato actin depolymerizing factor (ADF) proteins with those of Arabidopsis, rice and cotton. The 11 tomato ADF proteins are shown in red. The deduced full-length polypeptide sequences were used to create the tree. The tree was constructed by the Neighbor-joining method in MEGA 6.0 software following the Poisson-model. The bootstrap values were calculated as a percentage of 1000 replicates. Bootstrap values were shown next to the branches. The scale represents the units of the number of amino acid substitutions per site. Protein sequences of Arabidopsis, rice and cotton were taken from published literature, the TAIR, RAP-DB, Cottongen and the NCBI database.

Figure 4

Tissue specificity of tomato ADF gene expression: (a) Expression levels of the 11 ADF genes via quantitative PCR in different organs; root, stem, leaf, whole flower and fruit at six developmental stages (1 cm: 1 centimeter sized fruit; IM: immature fruit; MG: mature green fruit; B: breaker; B + 5: five days after breaker; B + 10: 10 days after breaker). The standard error of the means of three independent replicates is represented by the error bars. p values indicate statistically significant variations of expression. Different lowercase letters (a, b, c, etc.) indicate statistically significant difference. (b) Expression levels of the 11 ADF genes via quantitative PCR in the different floral organs; sepal, petal, stamen and ovary. The standard error of the means of three independent replicates is represented by the error bars. p values indicate the statistically significant variations of expression. Mean values at different sampling points are represented by different letters.

Figure 4

Tissue specificity of tomato ADF gene expression: (a) Expression levels of the 11 ADF genes via quantitative PCR in different organs; root, stem, leaf, whole flower and fruit at six developmental stages (1 cm: 1 centimeter sized fruit; IM: immature fruit; MG: mature green fruit; B: breaker; B + 5: five days after breaker; B + 10: 10 days after breaker). The standard error of the means of three independent replicates is represented by the error bars. p values indicate statistically significant variations of expression. Different lowercase letters (a, b, c, etc.) indicate statistically significant difference. (b) Expression levels of the 11 ADF genes via quantitative PCR in the different floral organs; sepal, petal, stamen and ovary. The standard error of the means of three independent replicates is represented by the error bars. p values indicate the statistically significant variations of expression. Mean values at different sampling points are represented by different letters.

Figure 5

Stress-related ADF gene expression in tomato. Expression levels of the 11 ADF genes via quantitative PCR under different stresses: (a) cold; (b) heat; (c) drought; (d) NaCl; (e) abscisic acid (ABA); (f) Jasmonic acid (JA); and (g) wounding. The standard error of the means of three independent replicates is represented by the error bars. P-values indicate the statistically significant variations of expression. Mean values at different sampling points are separated by different letters.