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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: The release of its genome sequence led to the development of high-resolution genomic tools, for both interspecific and intraspecific research, which has resulted in great advances in understanding Nasonia biology.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.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: The release of its genome sequence led to the development of high-resolution genomic tools, for both interspecific and intraspecific research, which has resulted in great advances in understanding Nasonia biology.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.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