2015
Adaptive Evolution of Eel Fluorescent Proteins from Fatty Acid Binding Proteins Produces Bright Fluorescence in the Marine Environment
Gruber DF, Gaffney JP, Mehr S, DeSalle R, Sparks JS, Platisa J, Pieribone VA. Adaptive Evolution of Eel Fluorescent Proteins from Fatty Acid Binding Proteins Produces Bright Fluorescence in the Marine Environment. PLOS ONE 2015, 10: e0140972. PMID: 26561348, PMCID: PMC4641735, DOI: 10.1371/journal.pone.0140972.Peer-Reviewed Original ResearchConceptsAcid-binding proteinFluorescent proteinFatty acid-binding proteinDuplication eventsGene duplication eventsStrong positive selectionNew fluorescent proteinsMarine environmentAdaptive evolutionEvolutionary switchCryptic genusVertebrate ordersVertebrate taxaPhylogenetic reconstructionProtein familyPhylogenetic analysisSequence motifsSister groupEvolutionary adaptationTranscriptomic analysisPositive selectionFatty acid binding proteinAcid binding proteinBinding proteinBright green fluorescenceTranscriptome sequencing and annotation of the polychaete Hermodice carunculata (Annelida, Amphinomidae)
Mehr S, Verdes A, DeSalle R, Sparks J, Pieribone V, Gruber DF. Transcriptome sequencing and annotation of the polychaete Hermodice carunculata (Annelida, Amphinomidae). BMC Genomics 2015, 16: 445. PMID: 26059236, PMCID: PMC4462082, DOI: 10.1186/s12864-015-1565-6.Peer-Reviewed Original ResearchConceptsOpen reading frameAvailable genomic dataHermodice carunculataGenomic dataDe novo transcriptome assemblyNon-model organismsNovo transcriptome assemblyDeep transcriptome sequencingCoral reef ecosystemsGene Ontology termsGene expression profilingKnowledge of reproductionTranscriptome assemblyReef organismsCoral diseasesGene discoveryPhylogenetic positionReef ecosystemsTranscriptome sequencingWestern Atlantic OceanPhylogenetic analysisH. carunculataOntology termsHomology searchImmune response genes
2009
Novel Internal Regions of Fluorescent Proteins Undergo Divergent Evolutionary Patterns
Gruber DF, DeSalle R, Lienau EK, Tchernov D, Pieribone VA, Kao HT. Novel Internal Regions of Fluorescent Proteins Undergo Divergent Evolutionary Patterns. Molecular Biology And Evolution 2009, 26: 2841-2848. PMID: 19770223, PMCID: PMC2775108, DOI: 10.1093/molbev/msp194.Peer-Reviewed Original ResearchConceptsFluorescent proteinStrong positive selection pressureDivergent evolutionary pressuresDivergent evolutionary patternsMolecular phylogenetic analysisSuperfamily of proteinsPositive selection pressureCyan fluorescent proteinGreen fluorescent proteinRed fluorescent proteinNatural functionMolecular evolutionPhylogenetic analysisEvolutionary patternsEvolutionary pressureSelection pressureProtein sequencesMarine organismsCompact proteinGeographic originNovel regionBiological researchProteinOrganismsInternal region