New targets acquired: improving locus recovery from the Angiosperms353 probe set

McLay, Todd G.B., Birch, Joanne L., Gunn, Bee F., Ning, Weixuan, Tate, Jennifer A., Nauheimer, Lars, Joyce, Elizabeth M., Simpson, Lalita, Schmidt-Lebuhn, Alexander N., Baker, William J., Forest, Félix, and Jackson, Chris J. (2021) New targets acquired: improving locus recovery from the Angiosperms353 probe set. Applications in Plant Sciences, 9 (7). e11420.

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Abstract

PREMISE: Universal target enrichment kits maximize utility across wide evolutionary breadth while minimizing the number of baits required to create a cost-efficient kit. The Angiosperms353 kit has been successfully used to capture loci throughout the angiosperms, but the default target reference file includes sequence information from only 6–18 taxa per locus. Consequently, reads sequenced from on-target DNA molecules may fail to map to references, resulting in fewer on-target reads for assembly, and reducing locus recovery.

METHODS: We expanded the Angiosperms353 target file, incorporating sequences from 566 transcriptomes to produce a ‘mega353’ target file, with each locus represented by 17–373 taxa. This mega353 file is a drop-in replacement for the original Angiosperms353 file in HybPiper analyses. We provide tools to subsample the file based on user-selected taxon groups, and to incorporate other transcriptome or protein-coding gene data sets.

RESULTS: Compared to the default Angiosperms353 file, the mega353 file increased the percentage of on-target reads by an average of 32%, increased locus recovery at 75% length by 49%, and increased the total length of the concatenated loci by 29%.

DISCUSSION: Increasing the phylogenetic density of the target reference file results in improved recovery of target capture loci. The mega353 file and associated scripts are available at: https://github.com/chrisjackson-pellicle/NewTargets.

Item ID: 70304
Item Type: Article (Research - C1)
ISSN: 2168-0450
Keywords: Angiosperms353, HybPiper, locus recovery, target capture, target file
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Copyright Information: © 2021 McLay et al. Applications in Plant Sciences published by Wiley Periodicals LLC on behalf of the Botanical Society of America. This is an open access article under the terms of the Creative Commons Attribution License, which permits use, distribution and reproduction in any medium, provided the original work is properly cited.
Date Deposited: 25 Jan 2022 02:59
FoR Codes: 31 BIOLOGICAL SCIENCES > 3104 Evolutionary biology > 310410 Phylogeny and comparative analysis @ 50%
31 BIOLOGICAL SCIENCES > 3108 Plant biology > 310899 Plant biology not elsewhere classified @ 50%
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