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Development of a Nasonia vitripennis outbred laboratory population for genetic analysis.

van de Zande L, Ferber S, de Haan A, Beukeboom LW, van Heerwaarden J, Pannebakker BA - Mol Ecol Resour (2013)

Bottom Line: As a characterization of its genetic composition, we provide data on the standing genetic variation and estimate the effective population size (N(e)) by microsatellite analysis.A genome-wide description of polymorphism is provided through pooled resequencing, which yielded 417,331 high-quality SNPs spanning all five Nasonia chromosomes.The HVRx population and its characterization are freely available as a community resource for investigators seeking to elucidate the genetic basis of complex trait variation using the Nasonia model system.

View Article: PubMed Central - PubMed

Affiliation: Evolutionary Genetics, Centre for Ecological and Evolutionary Studies, University of Groningen, 9700 CC, Groningen, the Netherlands.

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Genome-wide SNP density pattern in the Nasonia vitripennis HVRx outbred laboratory population. Mean SNP density adjusted for read depth in nonoverlapping 100 kb windows, plotted against chromosomal position.
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fig03: Genome-wide SNP density pattern in the Nasonia vitripennis HVRx outbred laboratory population. Mean SNP density adjusted for read depth in nonoverlapping 100 kb windows, plotted against chromosomal position.

Mentions: We found considerable genetic variability in the HVRx population, with a total of 417 331 SNPs distributed over the five chromosomes, or about 1 SNP per 796.7 bp [based on a physical genome size of 332.5 Mb (Gregory, 2013)]. SNP density varied between the chromosomes (one-way aov; F4,1880 = 9.58, P = 1.16e-07, Table3), with the lowest mean density per 100 kb window on chromosome 1. The pattern in SNP density differentiation is retained (one-way aov; F4,1880 = 1105.1, P < 2.2e-16, Table3, Fig. 3) upon adjusting for differences in read depth between the different chromosomes (one-way aov; F4,1880 = 12.268, P = 7.55e-10, Table3, Fig. S1, Supporting information). Interestingly, the highest SNP density per 100 kb window was also found on chromosome 1 at 25.3 Mb showing 438 SNPs (or 39.84 SNPS after adjusting for 10.99X read depth).


Development of a Nasonia vitripennis outbred laboratory population for genetic analysis.

van de Zande L, Ferber S, de Haan A, Beukeboom LW, van Heerwaarden J, Pannebakker BA - Mol Ecol Resour (2013)

Genome-wide SNP density pattern in the Nasonia vitripennis HVRx outbred laboratory population. Mean SNP density adjusted for read depth in nonoverlapping 100 kb windows, plotted against chromosomal position.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4260118&req=5

fig03: Genome-wide SNP density pattern in the Nasonia vitripennis HVRx outbred laboratory population. Mean SNP density adjusted for read depth in nonoverlapping 100 kb windows, plotted against chromosomal position.
Mentions: We found considerable genetic variability in the HVRx population, with a total of 417 331 SNPs distributed over the five chromosomes, or about 1 SNP per 796.7 bp [based on a physical genome size of 332.5 Mb (Gregory, 2013)]. SNP density varied between the chromosomes (one-way aov; F4,1880 = 9.58, P = 1.16e-07, Table3), with the lowest mean density per 100 kb window on chromosome 1. The pattern in SNP density differentiation is retained (one-way aov; F4,1880 = 1105.1, P < 2.2e-16, Table3, Fig. 3) upon adjusting for differences in read depth between the different chromosomes (one-way aov; F4,1880 = 12.268, P = 7.55e-10, Table3, Fig. S1, Supporting information). Interestingly, the highest SNP density per 100 kb window was also found on chromosome 1 at 25.3 Mb showing 438 SNPs (or 39.84 SNPS after adjusting for 10.99X read depth).

Bottom Line: As a characterization of its genetic composition, we provide data on the standing genetic variation and estimate the effective population size (N(e)) by microsatellite analysis.A genome-wide description of polymorphism is provided through pooled resequencing, which yielded 417,331 high-quality SNPs spanning all five Nasonia chromosomes.The HVRx population and its characterization are freely available as a community resource for investigators seeking to elucidate the genetic basis of complex trait variation using the Nasonia model system.

View Article: PubMed Central - PubMed

Affiliation: Evolutionary Genetics, Centre for Ecological and Evolutionary Studies, University of Groningen, 9700 CC, Groningen, the Netherlands.

Show MeSH