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Huang Z, Duan W, Song X, Tang J, Wu P, Zhang B, Hou X. Retention, Molecular Evolution, and Expression Divergence of the Auxin/Indole Acetic Acid and Auxin Response Factor Gene Families in Brassica Rapa Shed Light on Their Evolution Patterns in Plants. Genome Biol Evol 2015; 8:302-16. [PMID: 26721260 PMCID: PMC4779605 DOI: 10.1093/gbe/evv259] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
Auxin/indole acetic acids (Aux/IAAs) and auxin response factors (ARFs), major components of the Aux signaling network, are involved in many developmental processes in plants. Investigating their evolution will provide new sight on the relationship between the molecular evolution of these genes and the increasing morphotypes of plants. We constructed comparative analyses of the retention, structure, expansion, and expression patterns of Aux/IAAs and ARFs in Brassica rapa and their evolution in eight other plant species, including algae, bryophytes, lycophytes, and angiosperms. All 33 of the ARFs, including 1 ARF-like (AL) (a type of ARF-like protein) and 53 Aux/IAAs, were identified in the B. rapa genome. The genes mainly diverged approximately 13 Ma. After the split, no Aux/IAA was completely lost, and they were more preferentially retained than ARFs. In land plants, compared with ARFs, which increased in stability, Aux/IAAs expanded more rapidly and were under more relaxed selective pressure. Moreover, BraIAAs were expressed in a more tissue-specific fashion than BraARFs and demonstrated functional diversification during gene duplication under different treatments, which enhanced the cooperative interaction of homologs to help plants adapt to complex environments. In addition, ALs existed widely and had a closer relationship with ARFs, suggesting that ALs might be the initial structure of ARFs. Our results suggest that the rapid expansion and preferential retention of Aux/IAAs are likely paralleled by the increasingly complex morphotypes in Brassicas and even in land plants. Meanwhile, the data support the hypothesis that the PB1 domain plays a key role in the origin of both Aux/IAAs and ARFs.
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Affiliation(s)
- Zhinan Huang
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Key Laboratory of Biology and Germplasm Enhancement of Horticultural Crops in East China, College of Horticulture of Nanjing Agricultural University, Nanjing, P.R. China
| | - Weike Duan
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Key Laboratory of Biology and Germplasm Enhancement of Horticultural Crops in East China, College of Horticulture of Nanjing Agricultural University, Nanjing, P.R. China
| | - Xiaoming Song
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Key Laboratory of Biology and Germplasm Enhancement of Horticultural Crops in East China, College of Horticulture of Nanjing Agricultural University, Nanjing, P.R. China Center of Genomics and Computational Biology, College of Life Sciences, North China University of Science and Technology, Tangshan, Hebei, China
| | - Jun Tang
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Key Laboratory of Biology and Germplasm Enhancement of Horticultural Crops in East China, College of Horticulture of Nanjing Agricultural University, Nanjing, P.R. China
| | - Peng Wu
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Key Laboratory of Biology and Germplasm Enhancement of Horticultural Crops in East China, College of Horticulture of Nanjing Agricultural University, Nanjing, P.R. China
| | - Bei Zhang
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Key Laboratory of Biology and Germplasm Enhancement of Horticultural Crops in East China, College of Horticulture of Nanjing Agricultural University, Nanjing, P.R. China
| | - Xilin Hou
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Key Laboratory of Biology and Germplasm Enhancement of Horticultural Crops in East China, College of Horticulture of Nanjing Agricultural University, Nanjing, P.R. China
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Dong H, Liu D, Han T, Zhao Y, Sun J, Lin S, Cao J, Chen ZH, Huang L. Diversification and evolution of the SDG gene family in Brassica rapa after the whole genome triplication. Sci Rep 2015; 5:16851. [PMID: 26596461 PMCID: PMC4657036 DOI: 10.1038/srep16851] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2015] [Accepted: 10/21/2015] [Indexed: 12/21/2022] Open
Abstract
Histone lysine methylation, controlled by the SET Domain Group (SDG) gene family, is part of the histone code that regulates chromatin function and epigenetic control of gene expression. Analyzing the SDG gene family in Brassica rapa for their gene structure, domain architecture, subcellular localization, rate of molecular evolution and gene expression pattern revealed common occurrences of subfunctionalization and neofunctionalization in BrSDGs. In comparison with Arabidopsis thaliana, the BrSDG gene family was found to be more divergent than AtSDGs, which might partly explain the rich variety of morphotypes in B. rapa. In addition, a new evolutionary pattern of the four main groups of SDGs was presented, in which the Trx group and the SUVR subgroup evolved faster than the E(z), Ash groups and the SUVH subgroup. These differences in evolutionary rate among the four main groups of SDGs are perhaps due to the complexity and variability of the regions that bind with biomacromolecules, which guide SDGs to their target loci.
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Affiliation(s)
- Heng Dong
- Laboratory of Cell & Molecular Biology, Institute of Vegetable Science, Zhejiang University, Hangzhou, 310058, China
- Key Laboratory of Horticultural Plant Growth, Development and Quality Improvement, Ministry of Agriculture, Hangzhou, 310058, China
- Zhejiang Provincial Key Laboratory of Horticultural Plant Integrative Biology Hangzhou, 310058, China
| | - Dandan Liu
- Laboratory of Cell & Molecular Biology, Institute of Vegetable Science, Zhejiang University, Hangzhou, 310058, China
- Key Laboratory of Horticultural Plant Growth, Development and Quality Improvement, Ministry of Agriculture, Hangzhou, 310058, China
- Zhejiang Provincial Key Laboratory of Horticultural Plant Integrative Biology Hangzhou, 310058, China
| | - Tianyu Han
- Laboratory of Cell & Molecular Biology, Institute of Vegetable Science, Zhejiang University, Hangzhou, 310058, China
- Key Laboratory of Horticultural Plant Growth, Development and Quality Improvement, Ministry of Agriculture, Hangzhou, 310058, China
- Zhejiang Provincial Key Laboratory of Horticultural Plant Integrative Biology Hangzhou, 310058, China
| | - Yuxue Zhao
- Laboratory of Cell & Molecular Biology, Institute of Vegetable Science, Zhejiang University, Hangzhou, 310058, China
- Key Laboratory of Horticultural Plant Growth, Development and Quality Improvement, Ministry of Agriculture, Hangzhou, 310058, China
- Zhejiang Provincial Key Laboratory of Horticultural Plant Integrative Biology Hangzhou, 310058, China
| | - Ji Sun
- Wenzhou Vocational College of Science and Technology, Wenzhou, 325006, China
| | - Sue Lin
- Wenzhou Vocational College of Science and Technology, Wenzhou, 325006, China
| | - Jiashu Cao
- Laboratory of Cell & Molecular Biology, Institute of Vegetable Science, Zhejiang University, Hangzhou, 310058, China
- Key Laboratory of Horticultural Plant Growth, Development and Quality Improvement, Ministry of Agriculture, Hangzhou, 310058, China
- Zhejiang Provincial Key Laboratory of Horticultural Plant Integrative Biology Hangzhou, 310058, China
| | - Zhong-Hua Chen
- Department of Agronomy, Zhejiang Key Laboratory of Crop Germplasm, Zhejiang University, Hangzhou, 310058, China
- School of Science and Health, Western Sydney University, Penrith, NSW 2751, Australia
| | - Li Huang
- Laboratory of Cell & Molecular Biology, Institute of Vegetable Science, Zhejiang University, Hangzhou, 310058, China
- Key Laboratory of Horticultural Plant Growth, Development and Quality Improvement, Ministry of Agriculture, Hangzhou, 310058, China
- Zhejiang Provincial Key Laboratory of Horticultural Plant Integrative Biology Hangzhou, 310058, China
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