In silico karyotyping of chromosomally polymorphic malaria mosquitoes in the Anopheles gambiae complex
| Autor: | Vincenzo Petrarca, Marco Pombi, R. Rebecca Love, Nora J. Besansky, Seth Redmond, Alessandra della Torre, Beniamino Caputo |
|---|---|
| Jazyk: | angličtina |
| Rok vydání: | 2019 |
| Předmět: |
0106 biological sciences
Genetics 0303 health sciences education.field_of_study biology Anopheles gambiae Population Single-nucleotide polymorphism Tag SNP biology.organism_classification 010603 evolutionary biology 01 natural sciences Genome 3. Good health 03 medical and health sciences Genotype education Genotyping 030304 developmental biology Chromosomal inversion |
| DOI: | 10.1101/687566 |
| Popis: | Chromosomal inversion polymorphisms play an important role in adaptation to environmental heterogeneities. For mosquito species in theAnopheles gambiaecomplex 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 SNPs inside inversions whose biallelic genotype is strongly correlated with inversion genotype. We leveraged 1,347 fully sequencedAn. gambiaeandAnopheles coluzziigenomes 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 forin silicoinversion 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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