Identification of Auxin Response Factor (ARF) gene family in Echium plantagineum by Genome-wide analysis

Document Type : Research Paper

Authors

1 Plant Production and Genetics Department, Faculty of Agriculture, Shahid Chamran University of Ahvaz,, Ahvaz, Iran

2 Department of vegetables and irrigated pulse crop research, Seed and Plant Improvement Institute, Agricultural Research, Education and Extension Organization, Karaj, Iran.

10.22092/ijrfpbgr.2024.363113.1445

Abstract

Background and objectives:
Auxin response transcription factors (ARFs) are involved in auxin-mediated responses and play a key role in regulating the growth and development of plant nutrition, such as roots, stems, leaves, and reproductive organs, such as flowers and fruits. A genome-wide analysis of ARFs can improve the understanding of their regulatory role in the growth and development of our knowledge. Although the ARF gene family has been studied in some plant species, its structural features, molecular evolution, and expression profiling in Echium plantagineum are still unknown. This study aims to better understand distinctive structural and functional features among ARF proteins in E. plantagineum.
Methodology:
 In this study, a comprehensive genome-wide analysis was carried out to find All members of the ARF family in E. plantagineum based on two methods: 1) Hidden Markov Model (HMM) profiles of ARF gene family members and 2) Alignment with Arabidopsis (Arabidopsis thaliana) ARF genes sequence. ARF proteins were performed. The conserved motifs of ARF genes were identified, the chromosomal map and location of ARF genes were analyzed using a map chart, phylogenetic relationships using FastTree, and their protein characteristics were analyzed using the Expasy-ProtParam online server. To investigate the phylogenetic relationships of E. plantagineum ARF proteins, a phylogenetic tree was drawn using the alignment of E. plantagineum protein sequences.
Functional annotation and Gene Ontology classification were determined using the g: Profiler web server. The integrated network was predicted to identify co-expressed genes using the GeneMANIA web server.
Results:
 Based on genome-wide analysis, 28 ARF genes were identified, widely distributed in multiple chromosomes of E. plantagineum. These genes have a transcription regulatory activity, and depending on the nature of the sequence, they have an activating or repressing role. Subcellular location prediction showed that the ARF proteins are most present in the nucleus. Phylogenetic analysis of the 28 ARF proteins forms ten main classes; each class is specialized in function and provides insights into different orthologous relationships. The present study identifies the ARF gene family of E. plantagineum and its evolutionary relationship with the members of this family in Arabidopsis species. This issue can help identify ARF genes and reveal their function. Analysis of conserved motifs and domain search in ARF protein sequences showed that ARF proteins have DNA binding domains such as B3 and Auxin_resp domain in their structure. Chromosomal localization analysis showed that ARF members are widely distributed in chromosomes. The analysis of gene ontology terms (GO terms) in the biological process category showed that cellular process regulation, metabolic process regulation, stimulus-response, signaling, and biological regulation are the most significant GO terms.
Conclusion:
The results of this study provide a basis for identifying ARF genes and clarifying their function in 
E. plantagineum, which will be helpful for future research to discover and confirm the function of these genes.

Keywords

Main Subjects

References

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