{"doi":"10.1038/srep39031","title":"Imbalanced positive selection maintains the functional divergence of duplicated DIHYDROKAEMPFEROL 4-REDUCTASE genes","abstract":"<jats:title>Abstract</jats:title><jats:p>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<jats:italic>DIHYDROFLAVONOL 4-REDUCTASE</jats:italic>(<jats:italic>DFR</jats:italic>) has been reported in several organisms and may have been retained by escape from adaptive conflict (EAC). In this study, we screened the angiosperm<jats:italic>DFR</jats:italic>gene focusing on a diversified genus<jats:italic>Scutellaria</jats:italic>to investigate how these duplicated genes are retained. We deduced that gene duplication involved multiple independent events in angiosperms, but the duplication of<jats:italic>DFR</jats:italic>was before the divergence of<jats:italic>Scutellaria</jats:italic>. 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<jats:italic>DFR</jats:italic>duplicates in<jats:italic>Scutellaria</jats:italic>, implying adaptive subfunctionalization between duplicates. The discovery of pseudogenes accompanying a reduced replacement rate in one<jats:italic>DFR</jats:italic>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<jats:italic>DFR</jats:italic>gene in<jats:italic>Scutellaria</jats:italic>.</jats:p>","journal":"Scientific Reports","year":2016,"id":43771,"datarank":0.5079412363051905,"base_score":2.639057329615259,"endowment":2.639057329615259,"self_citation_contribution":0.3958585994422889,"citation_network_contribution":0.11208263686290154,"self_endowment_contribution":0.3958585994422889,"citer_contribution":0.11208263686290154,"corpus_percentile":null,"corpus_rank":null,"citation_count":13,"citer_count":11,"citers_with_citation_signal":3,"citers_with_endowment":3,"datacite_reuse_total":14,"is_dataset":false,"is_dataset_confidence":null,"is_data_producer":false,"deposit_databanks":null,"is_oa":false,"file_count":0,"downloads":0,"has_version_chain":false,"published_date":null,"fair_score":null,"fair_percentile":null,"algorithm_id":"datarank_citation_only_1hop_v6","ranking_scope":"data_only","authors":[{"id":207288,"name":"Yi-Wen Chen","orcid":null,"position":1,"is_corresponding":false},{"id":207289,"name":"Chia-Lung Huang","orcid":null,"position":2,"is_corresponding":false},{"id":165278,"name":"Jian Gao","orcid":null,"position":3,"is_corresponding":false},{"id":207290,"name":"Pei-Chun Liao","orcid":null,"position":4,"is_corresponding":false},{"id":207287,"name":"Bing-Hong Huang","orcid":null,"position":0,"is_corresponding":false}],"reference_count":0,"raw_metadata":{"has_enrichment":true,"base_score":2.639057329615259,"endowment":2.639057329615259,"datacite_reuse_total":14,"file_count":0,"downloads":0,"views":0,"has_version_chain":false,"is_dataset":false,"is_oa":false,"pmid":"27966614","pmcid":"PMC5155217","openalex_id":"https://openalex.org/W2565683002","authors":[],"funders":[],"total_grants":0,"fwci":0.3482,"citation_percentile":0.700067,"influential_citations":0,"citation_trend":[{"year":2017,"count":2},{"year":2020,"count":3},{"year":2022,"count":6},{"year":2023,"count":1},{"year":2025,"count":1}],"oa_status":"gold","license":"cc-by","oa_locations":[{"url":"https://doi.org/10.1038/srep39031","host_type":"journal"},{"url":"https://doi.org/10.1038/srep39031","host_type":"GOLD"},{"url":"https://doi.org/10.1038/srep39031","host_type":"publisher"},{"url":"https://www.nature.com/articles/srep39031.pdf","host_type":"publisher"},{"url":"https://www.nature.com/articles/srep39031","host_type":"publisher"},{"url":"https://pubmed.ncbi.nlm.nih.gov/27966614","host_type":"repository"},{"url":"https://www.ncbi.nlm.nih.gov/pmc/articles/5155217","host_type":"repository"},{"url":"https://europepmc.org/articles/PMC5155217","host_type":"Europe_PMC"},{"url":"https://europepmc.org/articles/PMC5155217?pdf=render","host_type":"Europe_PMC"}],"fields_of_study":["Photosynthetic Processes and Mechanisms","Plant biochemistry and biosynthesis","Plant Gene Expression Analysis","Medicine","Biology","Environmental Science","Alcohol Oxidoreductases","Codon","Evolution, Molecular","Gene Duplication","Gene Expression Profiling","Gene Expression Regulation, Plant","Genes, Duplicate","Genetic Variation","Magnoliopsida","Models, Genetic","Phylogeny","Plant Proteins","Regulatory Elements, Transcriptional","Scutellaria","Selection, Genetic"],"mesh_terms":["Alcohol Oxidoreductases","Codon","Models, Genetic","Phylogeny","Plant Proteins","Selection, Genetic","Genetic Variation","Gene Expression Regulation, Plant","Evolution, Molecular","Magnoliopsida","Genes, Duplicate","Gene Duplication","Gene Expression Profiling","Scutellaria","Regulatory Elements, Transcriptional"],"keywords":["Gene duplication","Functional divergence","Subfunctionalization","Biology","Gene","Pseudogene","Genetics","Gene family","Phylogenetic tree","Evolutionary biology","Copy-number variation","Gene 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