2019
In Silico Karyotyping of Chromosomally Polymorphic Malaria Mosquitoes in the Anopheles gambiae Complex
Love R, Redmond S, Pombi M, Caputo B, Petrarca V, della Torre A, Consortium T, Besansky N. In Silico Karyotyping of Chromosomally Polymorphic Malaria Mosquitoes in the Anopheles gambiae Complex. G3: Genes, Genomes, Genetics 2019, 9: 3249-3262. PMID: 31391198, PMCID: PMC6778791, DOI: 10.1534/g3.119.400445.Peer-Reviewed Original ResearchConceptsInversion genotypesSingle nucleotide polymorphismsInversion polymorphismTag single nucleotide polymorphismsChromosomal inversion polymorphismTag SNP genotypesAnopheles gambiae complexParacentric inversion polymorphismEnvironmental heterogeneityChromosomal rearrangementsImportant phenotypesMalaria mosquitoesSilico karyotypingNatural variationGambiae complexMosquito speciesTraditional cytogeneticsCytogenetic methodsBiallelic genotypesSignificant vectorSNP genotypesGonotrophic stagesNucleotide polymorphismsGenomeHuman malaria
2018
De Novo Mutations Resolve Disease Transmission Pathways in Clonal Malaria
Redmond SN, MacInnis BM, Bopp S, Bei AK, Ndiaye D, Hartl DL, Wirth DF, Volkman SK, Neafsey DE. De Novo Mutations Resolve Disease Transmission Pathways in Clonal Malaria. Molecular Biology And Evolution 2018, 35: 1678-1689. PMID: 29722884, PMCID: PMC5995194, DOI: 10.1093/molbev/msy059.Peer-Reviewed Original ResearchConceptsDe novo mutationsEvolutionary ratesSlow evolutionary rateNovo mutationsComplex life cycleSlow generation timeLow-complexity regionsGenomic regionsLarge genomesGenomic epidemiology approachReintroduction scenariosCombination of sequencingP. falciparumViral speciesMutation rateClonal lineagesGenomeMutation studiesLibrary preparationIdentical parasitesGeneration timeBacterial pathogensMalaria parasitesMutationsGenomic epidemiology
2013
The zebrafish reference genome sequence and its relationship to the human genome
Howe K, Clark M, Torroja C, Torrance J, Berthelot C, Muffato M, Collins J, Humphray S, McLaren K, Matthews L, McLaren S, Sealy I, Caccamo M, Churcher C, Scott C, Barrett J, Koch R, Rauch G, White S, Chow W, Kilian B, Quintais L, Guerra-Assunção J, Zhou Y, Gu Y, Yen J, Vogel J, Eyre T, Redmond S, Banerjee R, Chi J, Fu B, Langley E, Maguire S, Laird G, Lloyd D, Kenyon E, Donaldson S, Sehra H, Almeida-King J, Loveland J, Trevanion S, Jones M, Quail M, Willey D, Hunt A, Burton J, Sims S, McLay K, Plumb B, Davis J, Clee C, Oliver K, Clark R, Riddle C, Elliott D, Threadgold G, Harden G, Ware D, Begum S, Mortimore B, Kerry G, Heath P, Phillimore B, Tracey A, Corby N, Dunn M, Johnson C, Wood J, Clark S, Pelan S, Griffiths G, Smith M, Glithero R, Howden P, Barker N, Lloyd C, Stevens C, Harley J, Holt K, Panagiotidis G, Lovell J, Beasley H, Henderson C, Gordon D, Auger K, Wright D, Collins J, Raisen C, Dyer L, Leung K, Robertson L, Ambridge K, Leongamornlert D, McGuire S, Gilderthorp R, Griffiths C, Manthravadi D, Nichol S, Barker G, Whitehead S, Kay M, Brown J, Murnane C, Gray E, Humphries M, Sycamore N, Barker D, Saunders D, Wallis J, Babbage A, Hammond S, Mashreghi-Mohammadi M, Barr L, Martin S, Wray P, Ellington A, Matthews N, Ellwood M, Woodmansey R, Clark G, Cooper J, Tromans A, Grafham D, Skuce C, Pandian R, Andrews R, Harrison E, Kimberley A, Garnett J, Fosker N, Hall R, Garner P, Kelly D, Bird C, Palmer S, Gehring I, Berger A, Dooley C, Ersan-Ürün Z, Eser C, Geiger H, Geisler M, Karotki L, Kirn A, Konantz J, Konantz M, Oberländer M, Rudolph-Geiger S, Teucke M, Lanz C, Raddatz G, Osoegawa K, Zhu B, Rapp A, Widaa S, Langford C, Yang F, Schuster S, Carter N, Harrow J, Ning Z, Herrero J, Searle S, Enright A, Geisler R, Plasterk R, Lee C, Westerfield M, de Jong P, Zon L, Postlethwait J, Nüsslein-Volhard C, Hubbard T, Crollius H, Rogers J, Stemple D. The zebrafish reference genome sequence and its relationship to the human genome. Nature 2013, 496: 498-503. PMID: 23594743, PMCID: PMC3703927, DOI: 10.1038/nature12111.Peer-Reviewed Original ResearchConceptsHigh-quality sequence assembliesHuman protein-coding genesProtein-coding genesReference genome sequenceKey genomic featuresHuman reference genomeZebrafish genomeZebrafish orthologueReference genomeGenome sequenceHuman genomeSequence assemblyGenomic featuresLarge genesGenomeGenesOrthologuesVertebratesSequenceAssembly
2010
Widespread Divergence Between Incipient Anopheles gambiae Species Revealed by Whole Genome Sequences
Lawniczak M, Emrich S, Holloway A, Regier A, Olson M, White B, Redmond S, Fulton L, Appelbaum E, Godfrey J, Farmer C, Chinwalla A, Yang S, Minx P, Nelson J, Kyung K, Walenz B, Garcia-Hernandez E, Aguiar M, Viswanathan L, Rogers Y, Strausberg R, Saski C, Lawson D, Collins F, Kafatos F, Christophides G, Clifton S, Kirkness E, Besansky N. Widespread Divergence Between Incipient Anopheles gambiae Species Revealed by Whole Genome Sequences. Science 2010, 330: 512-514. PMID: 20966253, PMCID: PMC3674514, DOI: 10.1126/science.1195755.Peer-Reviewed Original ResearchMeSH KeywordsAnimalsAnophelesEvolution, MolecularFemaleGene FlowGenetic SpeciationGenome, InsectMaleModels, GeneticPolymorphism, Single NucleotideConceptsSpeciation processGenome sequencePrevious genome-wide scanHeterogeneous genomic divergenceAnopheles gambiae speciesGenome-wide scanUnknown genetic mechanismsWhole genome sequencesGene flowGenomic divergenceLarval ecologyGambiae speciesAnopheles gambiae sensu strictoPericentromeric regionGambiae sensu strictoGenetic mechanismsWidespread divergenceSensu strictoReproductive behaviorMajor vectorDivergenceSpeciationSequenceAppreciable levelsMolecular forms