2018
Uncovering Genomic Regions Associated with Trypanosoma Infections in Wild Populations of the Tsetse Fly Glossina fuscipes
Gloria-Soria A, Dunn WA, Yu X, Vigneron A, Lee KY, Li M, Weiss BL, Zhao H, Aksoy S, Caccone A. Uncovering Genomic Regions Associated with Trypanosoma Infections in Wild Populations of the Tsetse Fly Glossina fuscipes. G3: Genes, Genomes, Genetics 2018, 8: 887-897. PMID: 29343494, PMCID: PMC5844309, DOI: 10.1534/g3.117.300493.Peer-Reviewed Original ResearchConceptsGenomic resourcesRelated speciesCandidate genesNonmodel organismsTranscript librariesFunctional genomicsTranscriptome assemblyFunctional annotationWild populationsPhysiological traitsGenomic regionsDNA regulationMost speciesRNAseq experimentsGenetic basisLaboratory coloniesGenesFunctional studiesPolymorphic sitesSpeciesTrypanosome infection statusGenomeNew assemblyTrypanosoma infectionFlies
2016
Babesia microti from humans and ticks hold a genomic signature of strong population structure in the United States
Carpi G, Walter KS, Mamoun CB, Krause PJ, Kitchen A, Lepore TJ, Dwivedi A, Cornillot E, Caccone A, Diuk-Wasser MA. Babesia microti from humans and ticks hold a genomic signature of strong population structure in the United States. BMC Genomics 2016, 17: 888. PMID: 27821055, PMCID: PMC5100190, DOI: 10.1186/s12864-016-3225-x.Peer-Reviewed Original ResearchConceptsStrong population structurePopulation structureGenome-wide diversityDifferentiated genetic clustersRecent population expansionB. microti samplesTick-borne apicomplexan parasiteB. microtiNortheastern USAGene flowEvolutionary originApicomplexan parasitesApicoplast genomeGenetic clustersGenomic variationPopulation expansionGeographic rangeRange expansionGenomic signaturesCurrent diversityHuman-derived samplesInfectious phenotypeTick vectorCapture strategyDiversityPatterns of Genome-Wide Variation in Glossina fuscipes fuscipes Tsetse Flies from Uganda
Gloria-Soria A, Dunn WA, Telleria EL, Evans BR, Okedi L, Echodu R, Warren WC, Montague MJ, Aksoy S, Caccone A. Patterns of Genome-Wide Variation in Glossina fuscipes fuscipes Tsetse Flies from Uganda. G3: Genes, Genomes, Genetics 2016, 6: 1573-1584. PMID: 27172181, PMCID: PMC4889654, DOI: 10.1534/g3.116.027235.Peer-Reviewed Original ResearchMeSH KeywordsAnimalsChromosome MappingDNA, MitochondrialGene-Environment InteractionGenes, InsectGenetic LinkageGenetic VariationGenetics, PopulationGenome, InsectGenome-Wide Association StudyGenomicsGenotypeGeographyHigh-Throughput Nucleotide SequencingLinkage DisequilibriumMicrosatellite RepeatsPolymorphism, Single NucleotideSelection, GeneticTsetse FliesUgandaConceptsSingle nucleotide polymorphismsLinkage disequilibriumExtent of LDLocal environmental adaptationGenome-wide variationDetection of lociOverall linkage disequilibriumInsect vectorsDifferent environmental conditionsWhole-genome sequencingPopulation genomicsStrong selectionAssociation analysisEnvironmental adaptationGenomic patternsPopulation dynamicsSignificant genetic associationUninfected fliesDisease transmissionSequence technologyAssociation studiesEnvironmental conditionsTsetse fliesHuman African trypanosomiasisRelevant phenotypesDe Novo Genome Assembly Shows Genome Wide Similarity between Trypanosoma brucei brucei and Trypanosoma brucei rhodesiense
Sistrom M, Evans B, Benoit J, Balmer O, Aksoy S, Caccone A. De Novo Genome Assembly Shows Genome Wide Similarity between Trypanosoma brucei brucei and Trypanosoma brucei rhodesiense. PLOS ONE 2016, 11: e0147660. PMID: 26910229, PMCID: PMC4766357, DOI: 10.1371/journal.pone.0147660.Peer-Reviewed Original ResearchConceptsGenome assemblyGenetic recombinationT. bruceiPentatricopeptide repeat-containing proteinGenome-wide similarityDe novo genome assemblyHybrid de novo assemblyComparative genomic analysisRepeat-containing proteinVariant surface glycoprotein (VSG) coatComplete genome assemblyDe novo assemblyNovo genome assemblyGenomic differentiationSignificant epidemiological consequencesWhole-genome sequencingGene familyPutative genesEukaryotic pathogensNovo assemblySerum resistance associated geneHuman infective strainsGenomic analysisSingle geneAlcohol oxidoreductase
2014
Comparative Genomics Reveals Multiple Genetic Backgrounds of Human Pathogenicity in the Trypanosoma brucei Complex
Sistrom M, Evans B, Bjornson R, Gibson W, Balmer O, Mäser P, Aksoy S, Caccone A. Comparative Genomics Reveals Multiple Genetic Backgrounds of Human Pathogenicity in the Trypanosoma brucei Complex. Genome Biology And Evolution 2014, 6: 2811-2819. PMID: 25287146, PMCID: PMC4224348, DOI: 10.1093/gbe/evu222.Peer-Reviewed Original ResearchConceptsT. brucei complexGenomic variationLife historyVariable life historiesAverage linkage disequilibriumTrypanosoma brucei complexGenome-wide studiesMeiotic reciprocal recombinationWhole genome sequencesMultiple genetic backgroundsHuman pathogenicityNumber of subspeciesHuman-infective parasiteNuclear genomeComparative genomicsChromosome sizeEukaryotic parasitesGenomic regionsHuman African trypanosomiasisRegulatory genesTaxonomic designationsDiverse hostsSingle nucleotide polymorphismsGenetic variationReciprocal recombination
2011
Lineage Identification and Genealogical Relationships Among Captive Galápagos Tortoises
Benavides E, Russello M, Boyer D, Wiese R, Kajdacsi B, Marquez L, Garrick R, Caccone A. Lineage Identification and Genealogical Relationships Among Captive Galápagos Tortoises. Zoo Biology 2011, 31: 107-120. PMID: 21674601, DOI: 10.1002/zoo.20397.Peer-Reviewed Original ResearchConceptsGenealogical relationshipsGalápagos tortoisesEx situ conservation programsMicrosatellite genotypic dataSan Diego ZooGalápagos giant tortoisesWild-born individualsSitu conservation programsLevels of relatednessDetailed management recommendationsSanta Cruz IslandEvolutionary lineagesAssignment testsGenetic toolsSpecies designationRelated foundersGiant tortoisesGenotypic dataUnknown ancestryHaplotypic dataPedigree relationshipsDifferent speciesLineage identificationIsabela IslandConservation programs