Pushing the limits of whole genome amplification: Successful sequencing of RADseq libraries from single micro-hymenoptera (Chalcidoidea, Trichogramma)
A peer-reviewed article of this Preprint also exists.
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Abstract
A major obstacle to high-throughput genotyping of micro-hymenoptera is their small size. As species are difficult to discriminate and because complexes may exist, the sequencing of a pool of specimens is hazardous. Thus, one should be able to sequence pangenomic markers (e.g. RADtags) from a single specimen. To date, whole genome amplification (WGA) prior to library construction is still a necessity as only ca 10ng of DNA can be obtained from single specimens. However this amount of DNA is not compatible with manufacturer’s requirements for commercialised kits. Here we tested the accuracy of the GenomiPhi kit V2 on Trichogramma wasps by comparing RAD libraries obtained from the WGA of single specimens (generation F0 and F1, ca 1 ng input DNA for the WGA) and a biological amplification of genomic material (the pool of the progeny of the F1 generation). Globally, we found that ca 99% of the examined loci (up to 48,189; 109 bp each) were compatible with the mode of reproduction of the studied model (haplodiploidy) or a Mendelian inheritance of alleles. The remaining 1% (ca 0.01% of the analysed nucleotides) could represent WGA bias or other experimental / analytical bias. This study shows that the multiple displacement amplification method on which the GenomiPhi kit relies, could also be of great help for the high-throughput genotyping of micro-hymenoptera used for biological control or other organisms from which only a very low amount of DNA can be extracted such as human disease vectors (e.g. sand flies, fleas, ticks etc.).
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2018. Pushing the limits of whole genome amplification: Successful sequencing of RADseq libraries from single micro-hymenoptera (Chalcidoidea, Trichogramma) PeerJ Preprints 6:e26939v1 https://doi.org/10.7287/peerj.preprints.26939v1note This preprint is not peer-reviewed. You may wish to reference the subsequent peer-reviewed version of this article.
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This is a submission to PeerJ for review.
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Competing Interests
The authors declare that they have no competing interests.
Author Contributions
Astrid Cruaud conceived and designed the experiments, analyzed the data, prepared figures and/or tables, authored or reviewed drafts of the paper, approved the final draft.
Géraldine Groussier performed the experiments, contributed reagents/materials/analysis tools, approved the final draft.
Guenaëlle Genson performed the experiments, approved the final draft.
Laure Sauné performed the experiments, approved the final draft.
Jean-Yves Rasplus conceived and designed the experiments, analyzed the data, prepared figures and/or tables, authored or reviewed drafts of the paper, approved the final draft.
DNA Deposition
The following information was supplied regarding the deposition of DNA sequences:
Cleaned reads are available as a NCBI Sequence Read Archive (#SRP136713)
Data Deposition
The following information was supplied regarding data availability:
Cleaned reads are available as a NCBI Sequence Read Archive (#SRP136713)
Funding
This work was funded by the ANR project TriPTIC (ANR-14-CE18-0002). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.
