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New targets acquired: Improving locus recovery from the Angiosperms353 probe set.
- Source :
-
Applications in plant sciences [Appl Plant Sci] 2021 Jun 14; Vol. 9 (7). Date of Electronic Publication: 2021 Jun 14 (Print Publication: 2021). - Publication Year :
- 2021
-
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.<br />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.<br />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%.<br />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.<br /> (© 2021 McLay et al. Applications in Plant Sciences published by Wiley Periodicals LLC on behalf of the Botanical Society of America.)
Details
- Language :
- English
- ISSN :
- 2168-0450
- Volume :
- 9
- Issue :
- 7
- Database :
- MEDLINE
- Journal :
- Applications in plant sciences
- Publication Type :
- Academic Journal
- Accession number :
- 34336399
- Full Text :
- https://doi.org/10.1002/aps3.11420