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Research Article | Open Access

Large-scale analysis of the ARF and Aux/IAA gene families in 406 horticultural and other plants

Shuyan Feng1Nan Li1Huilong Chen2Zhuo Liu1Chunjin Li1Rong Zhou3Yingchao Zhang1Rui Cao1()Xiao Ma1,4()Xiaoming Song1()
School of Life Sciences/Library, North China University of Science and Technology, Tangshan, Hebei 063210, China
College of Grassland Science and Technology, China Agricultural University, Beijing 100193, China
Department of Food Science, Aarhus University, Aarhus 8200, Denmark
College of Horticultural Science & Technology, Hebei Normal University of Science & Technology, Qinhuangdao, Hebei 066600, China
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Abstract

The auxin response factor (ARF) and auxin/indole-3-acetic acid (Aux/IAA) family of genes are central components of the auxin signaling pathway and play essential roles in plant growth and development. Their large-scale analysis and evolutionary trajectory of origin are currently not known. Here, we identified the corresponding ARF and Aux/IAA family members and performed a large-scale analysis by scanning 406 plant genomes. The results showed that the ARF and Aux/IAA gene families originated from charophytes. The ARF family sequences were more conserved than the Aux/IAA family sequences. Dispersed duplications were the common expansion mode of ARF and Aux/IAA families in bryophytes, ferns, and gymnosperms; however, whole-genome duplication was the common expansion mode of the ARF and Aux/IAA families in basal angiosperms, magnoliids, monocots, and dicots. Expression and regulatory network analyses revealed that the Arabidopsis thaliana ARF and Aux/IAA families responded to multiple hormone, biotic, and abiotic stresses. The APETALA2 and serum response factor-transcription factor gene families were commonly enriched in the upstream and downstream genes of the ARF and Aux/IAA gene families. Our study provides a comprehensive overview of the evolutionary trajectories, structural functions, expansion mechanisms, expression patterns, and regulatory networks of these two gene families.

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Molecular Horticulture
Article number: 13
Cite this article:
Feng S, Li N, Chen H, et al. Large-scale analysis of the ARF and Aux/IAA gene families in 406 horticultural and other plants. Molecular Horticulture, 2024, 4(2): 13. https://doi.org/10.1186/s43897-024-00090-7
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