title: 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.
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.
authors.affiliation: 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.
authors.forename: Zhinan
authors.initials: Z
authors.lastname: Huang
authors.affiliation: 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.
authors.forename: Weike
authors.initials: W
authors.lastname: Duan
authors.affiliation: 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.
authors.forename: Xiaoming
authors.initials: X
authors.lastname: Song
authors.affiliation: 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.
authors.forename: Jun
authors.initials: J
authors.lastname: Tang
authors.affiliation: 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.
authors.forename: Peng
authors.initials: P
authors.lastname: Wu
authors.affiliation: 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.
authors.forename: Bei
authors.initials: B
authors.lastname: Zhang
authors.affiliation: 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 hxl@njau.edu.cn.
authors.forename: Xilin
authors.initials: X
authors.lastname: Hou
mesh_terms: D029741:Brassica rapa / Q000235:genetics* / Q000378:metabolism; D017124:Conserved Sequence; D056915:DNA Copy Number Variations; D004268:DNA-Binding Proteins / Q000235:genetics* / Q000378:metabolism; D019143:Evolution, Molecular; D007210:Indoleacetic Acids / Q000378:metabolism*; D010940:Plant Proteins / Q000235:genetics* / Q000378:metabolism; D059467:Transcriptome
chemical_list: D004268:DNA-Binding Proteins; D007210:Indoleacetic Acids; D010940:Plant Proteins
keywords: ARF; Brassica rapa; IAA; copy number variation; evolutionary pattern; expression divergence