Pushing the limits of whole genome amplification: successful sequencing of RADseq library from a single microhymenopteran (Chalcidoidea, Trichogramma )

A major obstacle to high-throughput genotyping of microhymenoptera 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...

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Bibliographic Details
Published in:PeerJ (San Francisco, CA) CA), 2018-10, Vol.6, p.e5640-e5640, Article e5640
Main Authors: Cruaud, Astrid, Groussier, Géraldine, Genson, Guenaëlle, Sauné, Laure, Polaszek, Andrew, Rasplus, Jean-Yves
Format: Article
Language:English
Subjects:
Accuracy
Bias
Biodiversity
Biological control
Deoxyribonucleic acid
DNA
DNA sequencing
Entomology
Environmental Sciences
Females
Genetic aspects
Genetic crosses
Genomes
Genomics
GenomiPhi
Genotyping
Heredity
High-throughput genotyping
Legal medicine
Life Sciences
Males
Microarthropods
Molecular Biology
Nucleotide sequencing
Nucleotides
RAD
Small amount of DNA
Taxonomy
Trichogramma
Vectors
Wasps
WGA
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Summary:A major obstacle to high-throughput genotyping of microhymenoptera 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 at most 10 ng of DNA can be obtained from single specimens (sometimes less). However, this amount of DNA is not compatible with manufacturer's requirements for commercial kits. Here we test the accuracy of the GenomiPhi kit V2 on wasps by comparing RAD libraries obtained from the WGA of single specimens (F0 and F1 generation, about1 ng input DNA for the WGA (0.17-2.9 ng)) and a biological amplification of genomic material (the pool of the progeny of the F1 generation). Globally, we found that 99% of the examined loci (up to 48,189 for one of the crosses, 109 bp each) were compatible with the mode of reproduction of the studied model (haplodiploidy) and Mendelian inheritance of alleles. The remaining 1% (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 microhymenoptera used for biological control, or other organisms from which only a very small amount of DNA can be extracted, such as human disease vectors (e.g.,  sandflies, fleas, ticks etc.).
ISSN:2167-8359
2167-8359
DOI:10.7717/peerj.5640