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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MDPI AG
2023-11-01
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| Series: | Plants |
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| Online Access: | https://www.mdpi.com/2223-7747/12/23/3943 |
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| author | Min Yan Yan Yan Ping Wang Yingping Wang Xiangmin Piao Peng Di Deok-Chun Yang |
| author_facet | Min Yan Yan Yan Ping Wang Yingping Wang Xiangmin Piao Peng Di Deok-Chun Yang |
| author_sort | Min Yan |
| collection | DOAJ |
| description | 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. |
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| issn | 2223-7747 |
| language | English |
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| spelling | doaj.art-deb43d8593c44c2e911d4c2d1a4e8e492023-12-08T15:23:43ZengMDPI AGPlants2223-77472023-11-011223394310.3390/plants12233943Genome-Wide Identification and Expression Analysis of Auxin Response Factor (ARF) Gene Family in <i>Panax ginseng</i> Indicates Its Possible Roles in Root DevelopmentMin Yan0Yan Yan1Ping Wang2Yingping Wang3Xiangmin Piao4Peng Di5Deok-Chun Yang6State Local Joint Engineering Research Center of Ginseng Breeding and Application, Jilin Agricultural University, Changchun 130118, ChinaState Local Joint Engineering Research Center of Ginseng Breeding and Application, Jilin Agricultural University, Changchun 130118, ChinaState Local Joint Engineering Research Center of Ginseng Breeding and Application, Jilin Agricultural University, Changchun 130118, ChinaState Local Joint Engineering Research Center of Ginseng Breeding and Application, Jilin Agricultural University, Changchun 130118, ChinaState Local Joint Engineering Research Center of Ginseng Breeding and Application, Jilin Agricultural University, Changchun 130118, ChinaState Local Joint Engineering Research Center of Ginseng Breeding and Application, Jilin Agricultural University, Changchun 130118, ChinaGraduate School of Biotechnology, College of Life Science, Kyung Hee University, Yongin-si 17104, Gyeonggi-do, Republic of KoreaAuxin-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.https://www.mdpi.com/2223-7747/12/23/3943<i>Panax ginseng</i>auxin response factor (ARF)root development |
| spellingShingle | Min Yan Yan Yan Ping Wang Yingping Wang Xiangmin Piao Peng Di Deok-Chun Yang 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 Plants <i>Panax ginseng</i> auxin response factor (ARF) root development |
| title | 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 |
| title_full | 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 |
| title_fullStr | 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 |
| title_full_unstemmed | 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 |
| title_short | 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 |
| title_sort | 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 |
| topic | <i>Panax ginseng</i> auxin response factor (ARF) root development |
| url | https://www.mdpi.com/2223-7747/12/23/3943 |
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