2024
A genotyping array for the globally invasive vector mosquito, Aedes albopictus
Cosme L, Corley M, Johnson T, Severson D, Yan G, Wang X, Beebe N, Maynard A, Bonizzoni M, Khorramnejad A, Martins A, Lima J, Munstermann L, Surendran S, Chen C, Maringer K, Wahid I, Mukherjee S, Xu J, Fontaine M, Estallo E, Stein M, Livdahl T, Scaraffia P, Carter B, Mogi M, Tuno N, Mains J, Medley K, Bowles D, Gill R, Eritja R, González-Obando R, Trang H, Boyer S, Abunyewa A, Hackett K, Wu T, Nguyễn J, Shen J, Zhao H, Crawford J, Armbruster P, Caccone A. A genotyping array for the globally invasive vector mosquito, Aedes albopictus. Parasites & Vectors 2024, 17: 106. PMID: 38439081, PMCID: PMC10910840, DOI: 10.1186/s13071-024-06158-z.Peer-Reviewed Original ResearchConceptsWhole-genome sequencingLow-coverage whole-genome sequencingSNP chipRepetitive elementsGenomic analysisNative rangePatterns of genomic variationWhole-genome sequencing dataSNP chip genotypesPopulation genomic analysesProtein-coding genesLevels of admixtureOrigin of invasionNon-coding regionsPercentage of repetitive elementsGenotyping of samplesChip genotypesGenetic clustersAncestry analysisGenomic variationGenotyping arraysGenotyping platformsMendelian genesGenetic variationGenotyping methods
2021
Demographic history and patterns of molecular evolution from whole genome sequencing in the radiation of Galapagos giant tortoises
Jensen E, Gaughran S, Garrick R, Russello M, Caccone A. Demographic history and patterns of molecular evolution from whole genome sequencing in the radiation of Galapagos giant tortoises. Molecular Ecology 2021, 30: 6325-6339. PMID: 34510620, DOI: 10.1111/mec.16176.Peer-Reviewed Original ResearchConceptsGalapagos giant tortoisesPopulation genetics theoryGiant tortoisesWhole-genome sequencingMolecular evolutionWhole genomeGenetic theoryGenome sequencingPopulation genetic summary statisticsGiant tortoise speciesPopulation genetic predictionsLife-history traitsSignals of selectionPatterns of diversityMutation accumulation ratesGenetic summary statisticsEvolutionary distinctivenessRecent radiationExtant lineagesPhylogeographic studiesHistory traitsPopulation genomicsEvolutionary historyMutation accumulationDemographic history
2016
Patterns 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 oxidoreductaseWhole genome sequencing shows sleeping sickness relapse is due to parasite regrowth and not reinfection
Richardson JB, Evans B, Pyana PP, Van Reet N, Sistrom M, Büscher P, Aksoy S, Caccone A. Whole genome sequencing shows sleeping sickness relapse is due to parasite regrowth and not reinfection. Evolutionary Applications 2016, 9: 381-393. PMID: 26834831, PMCID: PMC4721075, DOI: 10.1111/eva.12338.Peer-Reviewed Original ResearchSame patientHuman African trypanosomiasisHigh incidencePatientsTrypanosoma brucei gambienseHAT casesDrug resistanceDisease controlRelapseSingle nucleotide polymorphismsBrucei gambienseWhole-genome sequencingAfrican trypanosomiasisPathogenic levelsSaharan AfricaNucleotide polymorphismsOriginal strainRecent studiesTreatmentPromising new setFunctional studiesNovel insightsReinfectionFuture functional studiesNew strain