2021
Genomic analyses of new genes and their phenotypic effects reveal rapid evolution of essential functions in Drosophila development
Xia S, VanKuren NW, Chen C, Zhang L, Kemkemer C, Shao Y, Jia H, Lee U, Advani AS, Gschwend A, Vibranovski MD, Chen S, Zhang YE, Long M. Genomic analyses of new genes and their phenotypic effects reveal rapid evolution of essential functions in Drosophila development. PLOS Genetics 2021, 17: e1009654. PMID: 34242211, PMCID: PMC8270118, DOI: 10.1371/journal.pgen.1009654.Peer-Reviewed Original ResearchConceptsNew genesPhenotypic effectsEssential functionsLong evolutionary time scalesDevelopment of DrosophilaEvolutionary time scalesDrosophila developmentDrosophila genusEssential genesGene essentialityRNAi libraryYoung genesGenomic analysisCRISPR knockoutKnockout approachGenetic basisKnockdown experimentsComputational identificationGene effectsGenesDuplicate copiesRapid evolutionDrosophilaKnockdown efficiencyDistant ancestors
2013
New Gene Evolution: Little Did We Know
Long M, VanKuren NW, Chen S, Vibranovski MD. New Gene Evolution: Little Did We Know. Annual Review Of Genetics 2013, 47: 307-333. PMID: 24050177, PMCID: PMC4281893, DOI: 10.1146/annurev-genet-111212-133301.Peer-Reviewed Original ResearchMeSH KeywordsAnimalsBrainDrosophila melanogasterEvolution, MolecularForecastingGene DosageGene DuplicationGene Expression RegulationGene Regulatory NetworksGene Transfer, HorizontalGenesGenes, InsectGenes, PlantGenetic StructuresHumansMammalsModels, GeneticPhenotypePhylogenyRecombination, GeneticRNA, UntranslatedSelection, GeneticSex CharacteristicsTranscription, GeneticConceptsNew gene originationNew genesGene originationGenetic systemNew gene evolutionNew gene structuresGene evolutionPhenotypic evolutionGene structureDifferent organismsBiological diversityPhenotypic functionsGenesGenomeOriginationEvolutionDecades of effortOrganismsDiversityComprehensive pictureCritical component
2012
Adaptive Evolution and the Birth of CTCF Binding Sites in the Drosophila Genome
Ni X, Zhang YE, Nègre N, Chen S, Long M, White KP. Adaptive Evolution and the Birth of CTCF Binding Sites in the Drosophila Genome. PLOS Biology 2012, 10: e1001420. PMID: 23139640, PMCID: PMC3491045, DOI: 10.1371/journal.pbio.1001420.Peer-Reviewed Original ResearchMeSH KeywordsAdaptation, BiologicalAnimalsBase SequenceBinding SitesCCCTC-Binding FactorConserved SequenceDrosophilaDrosophila ProteinsEvolution, MolecularGenetic DriftGenetics, PopulationGenome, InsectOligonucleotide Array Sequence AnalysisPhylogenyProtein BindingRepressor ProteinsSelection, GeneticSpecies SpecificityTime FactorsConceptsCTCF binding siteDrosophila melanogasterNew genesCis-regulatory DNA sequencesGene expressionSpecies of DrosophilaGenome-wide bindingSignatures of selectionGenomes of humansComparative gene expression profilingGenome sequence dataRecent common ancestorGene expression profilingBinding sitesExpression divergenceGenome evolutionAdaptive evolutionDrosophila genomeDrosophila simulansEvolutionary ratesCTCF bindingCTCF proteinEvolutionary distanceNew CTCFCommon ancestor
2010
New Genes in Drosophila Quickly Become Essential
Chen S, Zhang YE, Long M. New Genes in Drosophila Quickly Become Essential. Science 2010, 330: 1682-1685. PMID: 21164016, PMCID: PMC7211344, DOI: 10.1126/science.1196380.Peer-Reviewed Original ResearchMeSH KeywordsAmino Acid SubstitutionAnimalsBody PatterningDrosophilaDrosophila melanogasterDrosophila ProteinsEvolution, MolecularGene DuplicationGene Expression ProfilingGene Expression Regulation, DevelopmentalGenes, EssentialGenes, InsectLarvaMetamorphosis, BiologicalPhenotypePhylogenyPupaRNA InterferenceTime FactorsWings, Animal
2003
RNA-dependent RNA polymerase gene sequence from foot-and-mouth disease virus in Hong Kong
Chen X, Feng Q, Wu Z, Liu Y, Huang K, Shi R, Chen S, Lu W, Ding M, Collins R, Fung Y, Lau L, Yu A, Chen J. RNA-dependent RNA polymerase gene sequence from foot-and-mouth disease virus in Hong Kong. Biochemical And Biophysical Research Communications 2003, 308: 899-905. PMID: 12927804, DOI: 10.1016/s0006-291x(03)01511-0.Peer-Reviewed Original ResearchMeSH KeywordsAmino Acid MotifsAmino Acid SequenceBase SequenceCloning, MolecularConserved SequenceDNA-Directed RNA PolymerasesFoot-and-Mouth Disease VirusGenetic VariationHong KongModels, GeneticMolecular Sequence DataMutationPhylogenyProtein Structure, TertiaryReverse Transcriptase Polymerase Chain ReactionRNA-Dependent RNA PolymeraseRNA, ViralSequence Analysis, DNASequence Homology, Amino AcidConceptsRNA-dependent RNA polymerase gene sequencesNucleotide sequenceRNA polymerase gene sequencesViral RNA-dependent RNA polymeraseRNA-dependent RNA polymeraseAmino acid sequenceAmino acid residuesMouth disease virusPolymerase gene sequencesCommon ancestorEvolutionary treeRNA polymeraseGene sequencesSequence comparisonAcid sequenceSame geneN-terminusDisease virusAcid residuesGenesFunctional relevanceRepresentative isolatesHost immune systemFMDV isolatesHKN/2002