New targets acquired: Improving locus recovery from the Angiosperms353 probe set
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...
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| Published in | Applications in plant sciences Vol. 9; no. 7 |
|---|---|
| Main Authors | , , , , , , , , , , , |
| Format | Journal Article |
| Language | English |
| Published |
United States
John Wiley & Sons, Inc
01.07.2021
John Wiley and Sons Inc Wiley |
| Subjects | |
| Online Access | Get full text |
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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. |
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| AbstractList | 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.
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.
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%.
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. 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. PREMISEUniversal 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.METHODSWe 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.RESULTSCompared 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%.DISCUSSIONIncreasing 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. 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.PREMISEUniversal 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.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.METHODSWe 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.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%.RESULTSCompared 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%.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.DISCUSSIONIncreasing 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. 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. |
| Author | Tate, Jennifer A. Gunn, Bee F. Simpson, Lalita Forest, Félix Baker, William J. Joyce, Elizabeth M. Schmidt‐Lebuhn, Alexander N. Ning, Weixuan Jackson, Chris J. Birch, Joanne L. Nauheimer, Lars McLay, Todd G. B. |
| AuthorAffiliation | 4 School of Fundamental Sciences Massey University Palmerston North New Zealand 2 School of Biosciences University of Melbourne Melbourne Australia 7 Royal Botanic Gardens, Kew Richmond Surrey TW9 3AE United Kingdom 1 National Herbarium of Victoria Royal Botanic Gardens Victoria Melbourne Australia 3 Centre for Australian National Biodiversity Research CSIRO Canberra Australia 6 Australian Tropical Herbarium James Cook University Cairns Australia 5 James Cook University Cairns Australia |
| AuthorAffiliation_xml | – name: 5 James Cook University Cairns Australia – name: 4 School of Fundamental Sciences Massey University Palmerston North New Zealand – name: 3 Centre for Australian National Biodiversity Research CSIRO Canberra Australia – name: 2 School of Biosciences University of Melbourne Melbourne Australia – name: 6 Australian Tropical Herbarium James Cook University Cairns Australia – name: 1 National Herbarium of Victoria Royal Botanic Gardens Victoria Melbourne Australia – name: 7 Royal Botanic Gardens, Kew Richmond Surrey TW9 3AE United Kingdom |
| Author_xml | – sequence: 1 givenname: Todd G. B. orcidid: 0000-0001-6405-8007 surname: McLay fullname: McLay, Todd G. B. email: todd.mclay@rbg.vic.gov.au organization: CSIRO – sequence: 2 givenname: Joanne L. orcidid: 0000-0002-8226-6085 surname: Birch fullname: Birch, Joanne L. organization: University of Melbourne – sequence: 3 givenname: Bee F. orcidid: 0000-0002-9591-3085 surname: Gunn fullname: Gunn, Bee F. organization: University of Melbourne – sequence: 4 givenname: Weixuan surname: Ning fullname: Ning, Weixuan organization: Massey University – sequence: 5 givenname: Jennifer A. orcidid: 0000-0001-5138-2115 surname: Tate fullname: Tate, Jennifer A. organization: Massey University – sequence: 6 givenname: Lars orcidid: 0000-0002-2847-0966 surname: Nauheimer fullname: Nauheimer, Lars organization: James Cook University – sequence: 7 givenname: Elizabeth M. orcidid: 0000-0001-8291-8058 surname: Joyce fullname: Joyce, Elizabeth M. organization: James Cook University – sequence: 8 givenname: Lalita orcidid: 0000-0003-3165-881X surname: Simpson fullname: Simpson, Lalita organization: James Cook University – sequence: 9 givenname: Alexander N. orcidid: 0000-0002-7402-8941 surname: Schmidt‐Lebuhn fullname: Schmidt‐Lebuhn, Alexander N. organization: CSIRO – sequence: 10 givenname: William J. orcidid: 0000-0001-6727-1831 surname: Baker fullname: Baker, William J. organization: Royal Botanic Gardens, Kew – sequence: 11 givenname: Félix orcidid: 0000-0002-2004-433X surname: Forest fullname: Forest, Félix organization: Royal Botanic Gardens, Kew – sequence: 12 givenname: Chris J. orcidid: 0000-0001-5785-6465 surname: Jackson fullname: Jackson, Chris J. organization: Royal Botanic Gardens Victoria |
| BackLink | https://www.ncbi.nlm.nih.gov/pubmed/34336399$$D View this record in MEDLINE/PubMed |
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| Copyright | 2021 McLay et al. published by Wiley Periodicals LLC on behalf of the Botanical Society of America. 2021 McLay et al. Applications in Plant Sciences published by Wiley Periodicals LLC on behalf of the Botanical Society of America. 2021. This work is published under http://creativecommons.org/licenses/by/4.0/ (the “License”). Notwithstanding the ProQuest Terms and Conditions, you may use this content in accordance with the terms of the License. |
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Universal target enrichment kits maximize utility across wide evolutionary breadth while minimizing the number of baits required to create a... Universal target enrichment kits maximize utility across wide evolutionary breadth while minimizing the number of baits required to create a cost-efficient... PREMISEUniversal target enrichment kits maximize utility across wide evolutionary breadth while minimizing the number of baits required to create a... PREMISE: Universal target enrichment kits maximize utility across wide evolutionary breadth while minimizing the number of baits required to create a... PREMISE Universal target enrichment kits maximize utility across wide evolutionary breadth while minimizing the number of baits required to create a... |
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| SubjectTerms | Angiosperms Angiosperms353 Application cost effectiveness DNA genes Genomes HybPiper loci locus recovery Nucleotide sequence Pellicle Phylogenetics Phylogeny Plant sciences target capture target file transcriptome Transcriptomes |
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| Title | New targets acquired: Improving locus recovery from the Angiosperms353 probe set |
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