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.

Genome-Wide Identification and Characterization of Actin-Depolymerizing Factor (ADF) Family Genes and Expression Analysis of Responses to Various Stresses in Zea Mays L.

“…MEGA7.0 was adopted to align the protein sequences and construct an unrooted phylogenetic tree by maximum likelihood method (Figure 4). In addition to the PhpADF (group I), the phylogenetic tree classified the ADF proteins into four main groups (group II, III, IV, V), consistent with published data of rice, Arabidopsis, and tomato [7,11]. In the phylogeny (Figure 4), group V included the largest numbers of ZmADFs proteins (ZmADF1/2/4/7/12/13), and five OsADFs also belonged to this group.…”

“…In this study, the phylogenetic classification of 36 ADF proteins from Physcomitrella patens, Arabidopsis thaliana, Oryza sativa japonica, and Zea mays were clustered into five groups. In addition to PhpADF (group I), the ADF proteins from Arabidopsis thaliana, Oryza sativa japonica, and Zea mays were classified into four main groups (group II, III, IV, V), consistent with published data of rice, Arabidopsis, and tomato [7,11]. Codon evolution of ADF genes has been investigated in relation to their putative functions.…”

“…SMART (http.//smart.embl-heidelberg.de/) software was adopted to determine whether the ADF-H domain existed in the candidate ADF genes. Finally, 13 ADF-H domain-containing genes (ZmADF1-ZmADF13) were identified in this study, the number of ADF genes identified in maize (13) was similar to Arabidopsis (11) and rice (11). We also analyzed the gene location, open reading frame (ORF) length, amino acids length, molecular weight, iso-electric point (PI), and grand average of hydropathy (GRAVY) ( Table 1).…”

“…Currently, the identification of whole-genome ADF gene family in many plants has been reported. For instance, there were 11 ADF genes in rice [7], 11 in Arabidopsis [8], 27 in banana [9], 14 in poplar [10], and 11 in tomato [11]. The phylogenetic analysis and expression profiling of higher-plant ADFs, such as Arabidopsis, rice, and tomato, has been reported, but not with the maize ADF gene family.…”

Actin Depolymerizing Factor Modulates Rhizobial Infection and Nodule Organogenesis in Common Bean

“…The size of the PvADF gene family in P. vulgaris is similar to that of other legumes (Table S1). Based on gene structure analysis, the coding region of each PvADF gene is organized in three exons ( Figure S1A), similar to the two-to three-exon organization of Glycine max ( Figure S1B), A. thaliana, and Solanum lycopersicum ADF genes [42,43]. In eight of the nine PvADF genes, the first or first few amino acids are encoded by a separate exon, as described for A. thaliana ADF genes [28].…”