Idioma:

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

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

Molecular ecology resources, 2014-09, Vol.14 (5), p.1000-1010 [Periódico revisado por pares]

England: Blackwell Publishing Ltd

Texto completo disponível

Citações Citado por

Enviar para

Título:
Sequence capture using PCR‐generated probes: a cost‐effective method of targeted high‐throughput sequencing for nonmodel organisms
Autor: Peñalba, Joshua V ; Smith, Lydia L ; Tonione, Maria A ; Sass, Chodon ; Hykin, Sarah M ; Skipwith, Phillip L ; McGuire, Jimmy A ; Bowie, Rauri C. K ; Moritz, Craig
Assuntos: Animals ; cost effectiveness ; DNA libraries ; Evolution ; genome ; Genomics - methods ; high-throughput nucleotide sequencing ; High-Throughput Nucleotide Sequencing - economics ; High-Throughput Nucleotide Sequencing - methods ; high-throughput sequencing ; Lizards - classification ; Lizards - genetics ; loci ; Oligonucleotide Probes - genetics ; Organisms ; Passeriformes - classification ; Passeriformes - genetics ; Phylogenetics ; phylogenomics ; Phylogeny ; phylogeography ; polymerase chain reaction ; Polymerase Chain Reaction - economics ; Polymerase Chain Reaction - methods ; population genetics ; sequence capture
É parte de: Molecular ecology resources, 2014-09, Vol.14 (5), p.1000-1010
Notas: http://dx.doi.org/10.1111/1755-0998.12249
istex:B9472DF5FF249BE54B240B0C4D517466789A736B
National Science Foundation and the Museum of Vertebrate Zoology
ark:/67375/WNG-DG3NZW9N-7
Figure S1 Comparison of coverage and sequence divergence. Figure S2 Comparison of coverage and probe length. Figure S3 Mitochondrial Capture Specificity. Table S1 Locus information for passerine project. Table S2 Locus information for Draco project. Table S3 Average coverage per locus for the passerine project (with flanking regions). Table S4 Average coverage per locus for the Enyalius project (with flanking regions). Table S5 Average coverage per locus for the Draco project (with flanking regions). Table S6 Average coverage per locus for the passerine project (without flanking regions). Table S7 Cost comparisons of SCPP and commercial probe kits. Table S8 SCPP Reagent Costs - Probe Generation & Hybridization. Table S9 SCPP Reagent Costs - Oligos. Table S10 Capture Assessment - qPCR. Appendix S1 Bioinformatics of read processing and phylogenetic methods for passerine tree.Appendix S2 Detailed protocol for SCPP.
ArticleID:MEN12249
ObjectType-Article-1
SourceType-Scholarly Journals-1
ObjectType-Feature-2
content type line 23
Descrição: 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 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.
Editor: England: Blackwell Publishing Ltd
Idioma: Inglês

Links

View this record in MEDLINE/PubMed

Voltar para lista de resultados

Realização: Logos de Redes Sociais:

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

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

England: Blackwell Publishing Ltd

Buscando em bases de dados remotas. Favor aguardar.