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Genome-wide patterns of polymorphism in an inbred line of the African malaria mosquito Anopheles gambiae.

Turissini DA, Gamez S, White BJ - Genome Biol Evol (2014)

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.

View Article: PubMed Central - PubMed

Affiliation: Department of Entomology, University of California, Riverside.

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Reductions in polymorphism are spatially heterogeneous across the genome. Black and red lines denote mean π for all SNPs in 1-Mb nonoverlapping windows across the genome for NGS and NGS INBRED, respectively. Boundaries of the 2La inversion are marked with a shaded box. Large, discrete blocks of both low and high nucleotide diversity in NGS INBRED are evident.
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evu243-F4: Reductions in polymorphism are spatially heterogeneous across the genome. Black and red lines denote mean π for all SNPs in 1-Mb nonoverlapping windows across the genome for NGS and NGS INBRED, respectively. Boundaries of the 2La inversion are marked with a shaded box. Large, discrete blocks of both low and high nucleotide diversity in NGS INBRED are evident.

Mentions: To compare polymorphism levels across the genome between NGS and NGS INBRED, we performed window-based analyses of π (fig. 4). Although diversity is markedly reduced in NGS INBRED relative to NGS in many regions, polymorphism levels nearly equal to those observed prior to inbreeding exist over discrete, large genomic intervals. For example, a region on 2L extending from 16 Mb proximal of the centromere all the way to the telomere shows only slightly reduced diversity in NGS INBRED. Another approximately 25-Mb region around the centromere of chromosome 3 shows little, if any, reduction in polymorphism. Inbreeding did not reduce π substantially in other smaller regions, such as near the telomere of 2R. The X chromosome shows a more spatially homogenous, albeit less dramatic, drop in diversity than the autosomes.Fig. 4.—


Genome-wide patterns of polymorphism in an inbred line of the African malaria mosquito Anopheles gambiae.

Turissini DA, Gamez S, White BJ - Genome Biol Evol (2014)

Reductions in polymorphism are spatially heterogeneous across the genome. Black and red lines denote mean π for all SNPs in 1-Mb nonoverlapping windows across the genome for NGS and NGS INBRED, respectively. Boundaries of the 2La inversion are marked with a shaded box. Large, discrete blocks of both low and high nucleotide diversity in NGS INBRED are evident.
© Copyright Policy - creative-commons
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4255774&req=5

evu243-F4: Reductions in polymorphism are spatially heterogeneous across the genome. Black and red lines denote mean π for all SNPs in 1-Mb nonoverlapping windows across the genome for NGS and NGS INBRED, respectively. Boundaries of the 2La inversion are marked with a shaded box. Large, discrete blocks of both low and high nucleotide diversity in NGS INBRED are evident.
Mentions: To compare polymorphism levels across the genome between NGS and NGS INBRED, we performed window-based analyses of π (fig. 4). Although diversity is markedly reduced in NGS INBRED relative to NGS in many regions, polymorphism levels nearly equal to those observed prior to inbreeding exist over discrete, large genomic intervals. For example, a region on 2L extending from 16 Mb proximal of the centromere all the way to the telomere shows only slightly reduced diversity in NGS INBRED. Another approximately 25-Mb region around the centromere of chromosome 3 shows little, if any, reduction in polymorphism. Inbreeding did not reduce π substantially in other smaller regions, such as near the telomere of 2R. The X chromosome shows a more spatially homogenous, albeit less dramatic, drop in diversity than the autosomes.Fig. 4.—

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.

View Article: PubMed Central - PubMed

Affiliation: Department of Entomology, University of California, Riverside.

Show MeSH
Related in: MedlinePlus