Genome-wide patterns of polymorphism in an inbred line of the African malaria mosquito Anopheles gambiae.
Bottom Line: We found that amenability to inbreeding varied between populations of A. gambiae.Although inbreeding dramatically reduced diversity across much of the genome, we discovered numerous, discrete genomic blocks that maintained high heterozygosity.Although creation of A. gambiae lines devoid of nearly all polymorphism may not be feasible, our results provide critical insights into how more fully isogenic lines can be created.
Affiliation: Department of Entomology, University of California, Riverside.Show MeSH
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Mentions: Overall, 90,049 or 57% of the total autosomal SNPs went from polymorphic in NGS to monomorphic in NGS INBRED. Polymorphism was reduced to a greater extent on the autosomes than the X, where only 4,394 or 40% of the total SNPs went from polymorphic in NGS to monomorphic in NGS INBRED (figs. 2 and 3). Specifically, average values of π per SNP on the autosomes declined from 0.30 in NGS to 0.12 in NGS INBRED. On the X chromosome, π per SNP only declined from 0.25 in NGS to 0.16 in NGS INBRED. Figure 3 plots π for individual SNPs in NGS versus NGS INBRED. As expected and detailed above, most SNPs went from polymorphic in NGS to monomorphic in NGS INBRED. However, a cluster of SNPs in the upper right-hand corner remained persistently polymorphic in both the NGS and NGS INBRED lines. SNPs in this category may exhibit strong heterosis, recessive lethality, or be linked with such sites, explaining their persistence at a frequency of approximately 50%. Alternatively, a small fraction of apparently heterozygous SNPs may actually be due to mapping errors where reads from two different genomic regions map to a single locus due to incomplete or improper reference genome assembly. Surprisingly, 7,155 SNPs appear monomorphic in NGS, but polymorphic in NGS INBRED. These SNPs were likely at a low frequency in NGS, were not present in our sample of 56 individuals, and increased in frequency during the inbreeding process.Fig. 2.—
Affiliation: Department of Entomology, University of California, Riverside.