title: Imbalanced positive selection maintains the functional divergence of duplicated DIHYDROKAEMPFEROL 4-REDUCTASE genes.
abstract: Gene duplication could be beneficial by functional division but might increase the risk of genetic load. The dynamics of duplicated paralogs number could involve recombination, positive selection, and functional divergence. Duplication of DIHYDROFLAVONOL 4-REDUCTASE (DFR) has been reported in several organisms and may have been retained by escape from adaptive conflict (EAC). In this study, we screened the angiosperm DFR gene focusing on a diversified genus Scutellaria to investigate how these duplicated genes are retained. We deduced that gene duplication involved multiple independent events in angiosperms, but the duplication of DFR was before the divergence of Scutellaria. Asymmetric positive selective pressures resulted in different evolutionary rates between the duplicates. Different numbers of regulatory elements, differential codon usages, radical amino acid changes, and differential gene expressions provide evidences of functional divergence between the two DFR duplicates in Scutellaria, implying adaptive subfunctionalization between duplicates. The discovery of pseudogenes accompanying a reduced replacement rate in one DFR paralogous gene suggested possibly leading to "loss of function" due to dosage imbalance after the transient adaptive subfunctionalization in the early stage of duplication. Notwithstanding, episodic gene duplication and functional divergence may be relevant to the diversification of ecological function of DFR gene in Scutellaria.
authors.affiliation: Department of Life Science, National Taiwan Normal University, Taipei 11677, Taiwan.
authors.forename: Bing-Hong
authors.initials: BH
authors.lastname: Huang
authors.affiliation: Department of Biological Science and Technology, National Pingtung University of Science and Technology, Pingtung 91201, Taiwan.
authors.forename: Yi-Wen
authors.initials: YW
authors.lastname: Chen
authors.affiliation: Department of Life Science, National Taiwan Normal University, Taipei 11677, Taiwan.
authors.forename: Chia-Lung
authors.initials: CL
authors.lastname: Huang
authors.affiliation: The Key Laboratory for Silviculture and Conservation of Ministry of Education, College of Forestry, Beijing Forestry University, Beijing 100083, China.
authors.forename: Jian
authors.initials: J
authors.lastname: Gao
authors.affiliation: Department of Life Science, National Taiwan Normal University, Taipei 11677, Taiwan.
authors.forename: Pei-Chun
authors.initials: PC
authors.lastname: Liao
mesh_terms: D000429:Alcohol Oxidoreductases / Q000235:genetics*; D003062:Codon / Q000235:genetics; D019143:Evolution, Molecular; D020440:Gene Duplication; D020869:Gene Expression Profiling; D018506:Gene Expression Regulation, Plant; D020131:Genes, Duplicate / Q000235:genetics*; D014644:Genetic Variation; D019684:Magnoliopsida / Q000145:classification / Q000201:enzymology / Q000235:genetics; D008957:Models, Genetic; D010802:Phylogeny; D010940:Plant Proteins / Q000235:genetics*; D050436:Regulatory Elements, Transcriptional; D031363:Scutellaria / Q000145:classification / Q000201:enzymology / Q000235:genetics; D012641:Selection, Genetic
chemical_list: D003062:Codon; D010940:Plant Proteins; D000429:Alcohol Oxidoreductases; C056570:dihydroflavanol 4-reductase