Large-scale analysis of the ARF and Aux/IAA gene families in 406 horticultural and other plants
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....
| Main Authors: | , , , , , , , , , |
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| Format: | Article |
| Language: | English |
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BMC
2024-04-01
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| Series: | Molecular Horticulture |
| Subjects: | |
| Online Access: | https://doi.org/10.1186/s43897-024-00090-7 |
| _version_ | 1797209094056050688 |
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| author | Shuyan Feng Nan Li Huilong Chen Zhuo Liu Chunjin Li Rong Zhou Yingchao Zhang Rui Cao Xiao Ma Xiaoming Song |
| author_facet | Shuyan Feng Nan Li Huilong Chen Zhuo Liu Chunjin Li Rong Zhou Yingchao Zhang Rui Cao Xiao Ma Xiaoming Song |
| author_sort | Shuyan Feng |
| collection | DOAJ |
| description | 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. |
| first_indexed | 2024-04-24T09:49:14Z |
| format | Article |
| id | doaj.art-cd3771121d184aa7a7eb7e0ece76289d |
| institution | Directory Open Access Journal |
| issn | 2730-9401 |
| language | English |
| last_indexed | 2024-04-24T09:49:14Z |
| publishDate | 2024-04-01 |
| publisher | BMC |
| record_format | Article |
| series | Molecular Horticulture |
| spelling | doaj.art-cd3771121d184aa7a7eb7e0ece76289d2024-04-14T11:29:18ZengBMCMolecular Horticulture2730-94012024-04-014111810.1186/s43897-024-00090-7Large-scale analysis of the ARF and Aux/IAA gene families in 406 horticultural and other plantsShuyan Feng0Nan Li1Huilong Chen2Zhuo Liu3Chunjin Li4Rong Zhou5Yingchao Zhang6Rui Cao7Xiao Ma8Xiaoming Song9School of Life Sciences/Library, North China University of Science and TechnologySchool of Life Sciences/Library, North China University of Science and TechnologyCollege of Grassland Science and Technology, China Agricultural UniversitySchool of Life Sciences/Library, North China University of Science and TechnologySchool of Life Sciences/Library, North China University of Science and TechnologyDepartment of Food Science, Aarhus UniversitySchool of Life Sciences/Library, North China University of Science and TechnologySchool of Life Sciences/Library, North China University of Science and TechnologySchool of Life Sciences/Library, North China University of Science and TechnologySchool of Life Sciences/Library, North China University of Science and TechnologyAbstract 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.https://doi.org/10.1186/s43897-024-00090-7ARFAux/IAALarge-scale analysisEvolutionary originDuplication type |
| spellingShingle | Shuyan Feng Nan Li Huilong Chen Zhuo Liu Chunjin Li Rong Zhou Yingchao Zhang Rui Cao Xiao Ma Xiaoming Song Large-scale analysis of the ARF and Aux/IAA gene families in 406 horticultural and other plants Molecular Horticulture ARF Aux/IAA Large-scale analysis Evolutionary origin Duplication type |
| title | Large-scale analysis of the ARF and Aux/IAA gene families in 406 horticultural and other plants |
| title_full | Large-scale analysis of the ARF and Aux/IAA gene families in 406 horticultural and other plants |
| title_fullStr | Large-scale analysis of the ARF and Aux/IAA gene families in 406 horticultural and other plants |
| title_full_unstemmed | Large-scale analysis of the ARF and Aux/IAA gene families in 406 horticultural and other plants |
| title_short | Large-scale analysis of the ARF and Aux/IAA gene families in 406 horticultural and other plants |
| title_sort | large scale analysis of the arf and aux iaa gene families in 406 horticultural and other plants |
| topic | ARF Aux/IAA Large-scale analysis Evolutionary origin Duplication type |
| url | https://doi.org/10.1186/s43897-024-00090-7 |
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