New targets acquired: Improving locus recovery from the Angiosperms353 probe set
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Date
14/06/2021
Open Access Location
Journal Title
Journal ISSN
Volume Title
Publisher
Botanical Society of America
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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.
Description
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Keywords
Angiosperms353, HybPiper, locus recovery, target capture, target file
Citation
APPLICATIONS IN PLANT SCIENCES, 2021, 9 (7)