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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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Polymorphism of the 2La inversion is responsible for the large block of polymorphism on NGS INBRED chromosome 2L. Different colored lines denote mean π for all SNPs in 1-Mb stepping windows across the genome for the three different karyotypes present in NGS INBRED. Boundaries of the 2La inversion are marked with a shaded box. Note the dramatic difference in polymorphism between heterokaryotypes and homokaryotypes.
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evu243-F5: Polymorphism of the 2La inversion is responsible for the large block of polymorphism on NGS INBRED chromosome 2L. Different colored lines denote mean π for all SNPs in 1-Mb stepping windows across the genome for the three different karyotypes present in NGS INBRED. Boundaries of the 2La inversion are marked with a shaded box. Note the dramatic difference in polymorphism between heterokaryotypes and homokaryotypes.

Mentions: To determine the effect of the segregating inversion on diversity, we performed window-based analyses of π for the three different karyotypes present in NGS and NGS INBRED (fig. 5). As expected diversity within homokaryotypes (2L+a or 2La) is near zero in NGS INBRED, but heterokaryotypes have high diversity. Thus, we conclude that persistence of the 2La inversion explains the large block of high diversity on the left arm of chromosome 2. Interestingly, when we perform window-based analyses of π on NGS individuals 2L+a homokaryotypes show markedly higher diversity than 2La homokaryotypes in the rearranged region (fig. 6). This pattern likely results from the colony being founded from eggs laid by multiple female mosquitoes from a population with a high frequency of the 2L+a arrangement. In contrast, the other blocks of extended heterozygosity do not overlap with known inversions. However, the second largest diversity block straddles the centromere of chromosome 3, a region of presumed low recombination that may functionally segregate as a single locus. Similar to the case for the 2La inversion, two divergent “centromere haplotypes” may be segregating in NGS and neither was lost through inbreeding.Fig. 5.—


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)

Polymorphism of the 2La inversion is responsible for the large block of polymorphism on NGS INBRED chromosome 2L. Different colored lines denote mean π for all SNPs in 1-Mb stepping windows across the genome for the three different karyotypes present in NGS INBRED. Boundaries of the 2La inversion are marked with a shaded box. Note the dramatic difference in polymorphism between heterokaryotypes and homokaryotypes.
© Copyright Policy - creative-commons
Related In: Results  -  Collection

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

evu243-F5: Polymorphism of the 2La inversion is responsible for the large block of polymorphism on NGS INBRED chromosome 2L. Different colored lines denote mean π for all SNPs in 1-Mb stepping windows across the genome for the three different karyotypes present in NGS INBRED. Boundaries of the 2La inversion are marked with a shaded box. Note the dramatic difference in polymorphism between heterokaryotypes and homokaryotypes.
Mentions: To determine the effect of the segregating inversion on diversity, we performed window-based analyses of π for the three different karyotypes present in NGS and NGS INBRED (fig. 5). As expected diversity within homokaryotypes (2L+a or 2La) is near zero in NGS INBRED, but heterokaryotypes have high diversity. Thus, we conclude that persistence of the 2La inversion explains the large block of high diversity on the left arm of chromosome 2. Interestingly, when we perform window-based analyses of π on NGS individuals 2L+a homokaryotypes show markedly higher diversity than 2La homokaryotypes in the rearranged region (fig. 6). This pattern likely results from the colony being founded from eggs laid by multiple female mosquitoes from a population with a high frequency of the 2L+a arrangement. In contrast, the other blocks of extended heterozygosity do not overlap with known inversions. However, the second largest diversity block straddles the centromere of chromosome 3, a region of presumed low recombination that may functionally segregate as a single locus. Similar to the case for the 2La inversion, two divergent “centromere haplotypes” may be segregating in NGS and neither was lost through inbreeding.Fig. 5.—

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