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An evaluation of pool-sequencing transcriptome-based exon capture for population genomics in non-model speciesuse asterix (*) to get italics
Emeline Deleury, Thomas Guillemaud, Aurélie Blin & Eric LombaertPlease use the format "First name initials family name" as in "Marie S. Curie, Niels H. D. Bohr, Albert Einstein, John R. R. Tolkien, Donna T. Strickland"
2020
<p>Exon capture coupled to high-throughput sequencing constitutes a cost-effective technical solution for addressing specific questions in evolutionary biology by focusing on expressed regions of the genome preferentially targeted by selection. Transcriptome-based capture, a process that can be used to capture the exons of non-model species, is used in phylogenomics. However, its use in population genomics remains rare due to the high costs of sequencing large numbers of indexed individuals across multiple populations. We evaluated the feasibility of combining transcriptome-based capture and the pooling of tissues from numerous individuals for DNA extraction as a cost-effective, generic and robust approach to estimating the variant allele frequencies of any species at the population level. We designed capture probes for ~5 Mb of chosen de novo transcripts from the Asian ladybird Harmonia axyridis (5,717 transcripts). We called ~300,000 bi-allelic SNPs for a pool of 36 non-indexed individuals. Capture efficiency was high, and pool-seq was as effective and accurate as individual-seq for detecting variants and estimating allele frequencies. Finally, we also evaluated an approach for simplifying bioinformatic analyses by mapping genomic reads directly to targeted transcript sequences to obtain coding variants. This approach is effective and does not affect the estimation of SNP allele frequencies, except for a small bias close to some exon ends. We demonstrate that this approach can also be used to predict the intron-exon boundaries of targeted de novo transcripts, making it possible to abolish genotyping biases near exon ends.</p>
https://doi.org/10.5281/zenodo.2598388You should fill this box only if you chose 'All or part of the results presented in this preprint are based on data'. URL must start with http:// or https://
https://doi.org/10.1101/583534You should fill this box only if you chose 'Scripts were used to obtain or analyze the results'. URL must start with http:// or https://
You should fill this box only if you chose 'Codes have been used in this study'. URL must start with http:// or https://
Target enrichment; Non-model organism; Population genomics; Pool-sequencing; Harmonia axyridis; Intron-exon boundary prediction
NonePlease indicate the methods that may require specialised expertise during the peer review process (use a comma to separate various required expertises).
Bioinformatics, Population genomics
No need for them to be recommenders of PCI Genomics. Please do not suggest reviewers for whom there might be a conflict of interest. Reviewers are not allowed to review preprints written by close colleagues (with whom they have published in the last four years, with whom they have received joint funding in the last four years, or with whom they are currently writing a manuscript, or submitting a grant proposal), or by family members, friends, or anyone for whom bias might affect the nature of the review - see the code of conduct
e.g. John Doe [john@doe.com]
2020-02-26 09:21:11
Thomas Derrien