Genome–Wide Identification and Functional Characterization of Auxin Response Factor (ARF) Genes in Eggplant

Abstract

Auxin response factors (ARFs) are important plant transcription factors that are differentially expressed in response to auxin and various abiotic stresses. ARFs play important roles in mediating plant growth and stress responses; however, these factors have not been studied in eggplants. In this study, genome–wide identification and the functional analysis of the ARF gene family in eggplants (Solanum melongena L.) were performed. A total of 20 ARF (SmARF) genes were identified and phylogenetically classified into three groups. Our analysis revealed four functional domains and 10 motifs in these proteins. Subcellular localization showed that the SmARFs localized in the nucleus. To investigate the biological functions of the SmARFs under 2,4–D and salt stress treatments, quantitative real–time RT–PCR (qRT–PCR) was conducted. Most SmARF genes exhibited changes in expression in response to 2,4–D treatments in the flowers, especially SmARF4 and 7B. All SmARF genes quickly responded to salt stress, except SmARF17 and 19 in leaves, SmARF1A and 7B in roots, and SmARF2A, SmARF7B, and SmARF16B in stems. These results helped to elucidate the role of ARFs in auxin signaling under 2,4–D and salt stress in eggplants.

Genome-wide identification and expression analysis of ARF gene family in embryonic development of Korean pine (Pinus koraiensis)

“…The results revealed that all ARF proteins were classified into 6 subfamilies, with Group IIId consisting solely of AtARFs. This finding is consistent with previous studies on ARF genes in poplar [ 62 ], and eggplant ( Solanum melongena ) [ 63 ], suggesting significant changes in the functions of AtARF family members in Group IIId during species evolution. Group II contained the highest number of ARF genes from Korean pine and Populus (Fig.…”

Genome-wide identification and expression analysis of the Auxin-Response factor (ARF) gene family in Medicago sativa under abiotic stress

“…This result indicates that the MsARF family proteins have better hydrophilicity. As transcription factors, ARF proteins usually function in the nucleus [ 7 ]. Consistent with the subcellular localization results reported in other species, such as eggplant [ 7 ], tomato [ 46 ], and maize [ 41 ], the subcellular predictions indicate that most of the MsARF genes were localized to the nucleus.…”

“…As transcription factors, ARF proteins usually function in the nucleus [ 7 ]. Consistent with the subcellular localization results reported in other species, such as eggplant [ 7 ], tomato [ 46 ], and maize [ 41 ], the subcellular predictions indicate that most of the MsARF genes were localized to the nucleus. In addition, no MsARF genes were found to have any conducting peptides, signal peptides, or transmembrane structures, indicating that the 50 MsARF genes located in the nucleus did not secrete or transport but only regulated gene expression in the nucleus.…”

“…Although the number of motif members varied among clades, the group motif patterns were strongly conserved. The comparison of novel functional domains or motif sequences across multiple homologous proteins has been a widely used method to predict protein function based on evolutionary conservation [ 7 ]. We found that motif 8 was highly conserved in the MsARF gene family.…”

“…Numerous plants, including Arabidopsis thaliana , have a large number of functional genes that are auxin-regulated and play a significant role in growth and development [ 3 – 5 ]. Among these genes, auxin response factor (ARF) family members play a vital role in auxin signaling and regulating the expression of auxin-responsive genes [ 6 , 7 ]. Most ARFs contain three conserved functional domains: the DNA binding domain (DBD) at the N terminus, the variable intermediate region (MR) acting as the activating domain (AD) or inhibitory domain (RD), and the C-terminal dimerization domain (CTD) [ 8 ].…”