In Silico Karyotyping of Chromosomally Polymorphic Malaria Mosquitoes in the Anopheles gambiae Complex
| Autor: | Love, R. Rebecca, Redmond, Seth, Pombi, Marco, Caputo, Beniamino, Petrarca, Vincenzo, Della Torre, Alessandra, Anopheles gambiae 1000 Genomes Consortium (including MC Fontaine), The, Besansky, Nora |
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| Přispěvatelé: | University of Notre Dame [Indiana] (UND), Broad Institute [Cambridge], Harvard University [Cambridge]-Massachusetts Institute of Technology (MIT), Department of Public Health and Infectious Diseases, Institut Pasteur, Fondation Cenci Bolognetti - Istituto Pasteur Italia, Fondazione Cenci Bolognetti, Réseau International des Instituts Pasteur (RIIP)-Réseau International des Instituts Pasteur (RIIP)-Università degli Studi di Roma 'La Sapienza' = Sapienza University [Rome], This work was supported by the National Institutes of Health (R01 AI125360 awarded to NJB). During this work, NJB was supported by Target Malaria, which receives core funding from the Bill & Melinda Gates Foundation and from the Open Philanthropy Project Fund, an advised fund of Silicon Valley Community Foundation. |
| Jazyk: | angličtina |
| Rok vydání: | 2019 |
| Předmět: |
single nucleotide
0106 biological sciences genotype Anopheles gambiae chromosomal inversion polymorphism QH426-470 01 natural sciences Genome polymorphism malaria vector inversion genotyping [SDV.MHEP.MI]Life Sciences [q-bio]/Human health and pathology/Infectious diseases Genotype karyotype analysis humans Genetics (clinical) Chromosomal inversion Genetics 0303 health sciences education.field_of_study [SDV.BID.EVO]Life Sciences [q-bio]/Biodiversity/Populations and Evolution [q-bio.PE] karyotyping Tag SNP 3. Good health animals chromosome inversion tag SNP chromosomes Population malaria Single-nucleotide polymorphism Biology mosquito vectors 010603 evolutionary biology 03 medical and health sciences evolution genomics molecular education Molecular Biology Genotyping 030304 developmental biology biology.organism_classification genetic variation anopheles gambiae tag snp anopheles evolution molecular polymorphism single nucleotide reproducibility of results chromosomes insect polymorphism genetic insect genetic [SDE.BE]Environmental Sciences/Biodiversity and Ecology |
| Zdroj: | G3 G3, Genetics Society of America, 2019, 9 (10), pp.3249-3262. ⟨10.1534/g3.119.400445⟩ G3: Genes, Genomes, Genetics, Vol 9, Iss 10, Pp 3249-3262 (2019) |
| ISSN: | 2160-1836 |
| DOI: | 10.1534/g3.119.400445⟩ |
| Popis: | Chromosomal inversion polymorphisms play an important role in adaptation to environmental heterogeneities. For mosquito species in the Anopheles gambiae complex that are significant vectors of human malaria, paracentric inversion polymorphisms are abundant and are associated with ecologically and epidemiologically important phenotypes. Improved understanding of these traits relies on determining mosquito karyotype, which currently depends upon laborious cytogenetic methods whose application is limited both by the requirement for specialized expertise and for properly preserved adult females at specific gonotrophic stages. To overcome this limitation, we developed sets of tag single nucleotide polymorphisms (SNPs) inside inversions whose biallelic genotype is strongly correlated with inversion genotype. We leveraged 1,347 fully sequenced An. gambiae and Anopheles coluzzii genomes in the Ag1000G database of natural variation. Beginning with principal components analysis (PCA) of population samples, applied to windows of the genome containing individual chromosomal rearrangements, we classified samples into three inversion genotypes, distinguishing homozygous inverted and homozygous uninverted groups by inclusion of the small subset of specimens in Ag1000G that are associated with cytogenetic metadata. We then assessed the correlation between candidate tag SNP genotypes and PCA-based inversion genotypes in our training sets, selecting those candidates with >80% agreement. Our initial tests both in held-back validation samples from Ag1000G and in data independent of Ag1000G suggest that when used for in silico inversion genotyping of sequenced mosquitoes, these tags perform better than traditional cytogenetics, even for specimens where only a small subset of the tag SNPs can be successfully ascertained. |
| Databáze: | OpenAIRE |
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