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Sequence capture using PCR-generated probes: A cost-effective method of targeted high-throughput sequencing for nonmodel organisms

Penalba, Joshua V.; Smith, Lydia L.; Tonione, M.; Sass, Chodon; Hykin, Sarah M.; Skipwith, Phillip L.; McGuire, Jimmy A; Bowie, Rauri C K; Moritz, Craig

Description

Recent advances in high-throughput sequencing library preparation and subgenomic enrichment methods have opened new avenues for population genetics and phylogenetics of nonmodel organisms. To multiplex large numbers of indexed samples while sequencing predominantly orthologous, targeted regions of the genome, we propose modifications to an existing, in-solution capture that utilizes PCR products as target probes to enrich library pools for the genomic subset of interest. The sequence capture...[Show more]

dc.contributor.authorPenalba, Joshua V.
dc.contributor.authorSmith, Lydia L.
dc.contributor.authorTonione, M.
dc.contributor.authorSass, Chodon
dc.contributor.authorHykin, Sarah M.
dc.contributor.authorSkipwith, Phillip L.
dc.contributor.authorMcGuire, Jimmy A
dc.contributor.authorBowie, Rauri C K
dc.contributor.authorMoritz, Craig
dc.date.accessioned2015-12-13T22:30:56Z
dc.identifier.issn1755-098X
dc.identifier.urihttp://hdl.handle.net/1885/75067
dc.description.abstractRecent advances in high-throughput sequencing library preparation and subgenomic enrichment methods have opened new avenues for population genetics and phylogenetics of nonmodel organisms. To multiplex large numbers of indexed samples while sequencing predominantly orthologous, targeted regions of the genome, we propose modifications to an existing, in-solution capture that utilizes PCR products as target probes to enrich library pools for the genomic subset of interest. The sequence capture using PCR-generated probes (SCPP) protocol requires no specialized equipment, is highly flexible and significantly reduces experimental costs for projects where a modest scale of genetic data is optimal (25-100 genomic loci). Our alterations enable application of this method across a wider phylogenetic range of taxa and result in higher capture efficiencies and coverage at each locus. Efficient and consistent capture over multiple SCPP experiments and at various phylogenetic distances is demonstrated, extending the utility of this method to both phylogeographic and phylogenomic studies.
dc.publisherWiley-Blackwell
dc.sourceMolecular Ecology Resources
dc.titleSequence capture using PCR-generated probes: A cost-effective method of targeted high-throughput sequencing for nonmodel organisms
dc.typeJournal article
local.description.notesImported from ARIES
local.identifier.citationvolume14
dc.date.issued2014
local.identifier.absfor060411 - Population, Ecological and Evolutionary Genetics
local.identifier.ariespublicationU3488905xPUB4450
local.type.statusPublished Version
local.contributor.affiliationPenalba, Joshua V., University of California
local.contributor.affiliationSmith, Lydia L., University of California
local.contributor.affiliationTonione, M., University of California
local.contributor.affiliationSass, Chodon, University of California
local.contributor.affiliationHykin, Sarah M., University of California
local.contributor.affiliationSkipwith, Phillip L., University of California
local.contributor.affiliationMcGuire, Jimmy A, University of California
local.contributor.affiliationBowie, Rauri C K, University of California
local.contributor.affiliationMoritz, Craig, College of Medicine, Biology and Environment, ANU
local.description.embargo2037-12-31
local.bibliographicCitation.issue5
local.bibliographicCitation.startpage1000
local.bibliographicCitation.lastpage1010
local.identifier.doi10.1111/1755-0998.12249
local.identifier.absseo970106 - Expanding Knowledge in the Biological Sciences
dc.date.updated2015-12-11T08:57:59Z
local.identifier.scopusID2-s2.0-84905988798
local.identifier.thomsonID000340425100011
CollectionsANU Research Publications

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