Genome-Wide Identification and Expression Analysis of Auxin Response Factor (ARF) Gene Family in <i>Panax ginseng</i> Indicates Its Possible Roles in Root Development

Auxin-responsive factors (ARFs) are an important class of transcription factors and are an important component of auxin signaling. This study conducted a genome-wide analysis of the ARF gene family in ginseng and presented its findings. Fifty-three ARF genes specific to ginseng (<i>PgARF</i...

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Bibliographic Details
Main Authors: Min Yan, Yan Yan, Ping Wang, Yingping Wang, Xiangmin Piao, Peng Di, Deok-Chun Yang
Format: Article
Language:English
Published: MDPI AG 2023-11-01
Series:Plants
Subjects:
Online Access:https://www.mdpi.com/2223-7747/12/23/3943
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Summary:Auxin-responsive factors (ARFs) are an important class of transcription factors and are an important component of auxin signaling. This study conducted a genome-wide analysis of the ARF gene family in ginseng and presented its findings. Fifty-three ARF genes specific to ginseng (<i>PgARF</i>) were discovered after studying the ginseng genome. The coding sequence (CDS) has a length of 1092–4098 base pairs and codes for a protein sequence of 363–1565 amino acids. Among them, <i>PgARF32</i> has the least number of exons (2), and <i>PgARF16</i> has the most exons (18). These genes were then distributed into six subgroups based on the results obtained from phylogenetic analysis. In each subgroup, the majority of the <i>PgARF</i> genes displayed comparable intron/exon structures. <i>PgARF</i> genes are unevenly distributed on 20 chromosomes. Most PgARFs have B3 DNA binding, Auxin_resp, and PB1 domains. The <i>PgARF</i> promoter region contains various functional domains such as plant hormones, light signals, and developmental functions. Segmental duplications contribute to the expansion of the <i>ARF</i> gene family in ginseng, and the genes have undergone purifying selection during evolution. Transcriptomic results showed that some <i>PgARFs</i> had different expression patterns in different parts of ginseng; most <i>PgARFs</i> were affected by exogenous hormones, and a few <i>PgARFs</i> responded to environmental stress. It is suggested that <i>PgARF</i> is involved in the development of ginseng by regulating hormone-mediated genes. <i>PgARF14</i>, <i>PgARF42</i>, and <i>PgARF53</i> are all situated in the nucleus, and both <i>PgARR14</i> and <i>PgARF53</i> noticeably enhance the growth length of roots in Arabidopsis. Our findings offer a theoretical and practical foundation for exploring <i>PgARFs</i>’ role in the growth of ginseng roots.
ISSN:2223-7747