ArticleBMC genomics2012
Targeted enrichment of the black cottonwood (Populus trichocarpa) gene space using sequence capture.
Article in BMC genomics, 2012. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 35 papers.
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Who cites it
35 citing papers in PubMed.
- NewtCap: An Efficient Target Capture Approach to Boost Genomic Studies in Salamandridae (True Salamanders and Newts).Ecology and evolution · 2025Article
- Targeted metagenomics using bait-capture to detect antibiotic resistance genes in retail meat and seafood.Frontiers in microbiology · 2023Article
- Genomic selection in tropical perennial crops and plantation trees: a review.Molecular breeding : new strategies in plant improvement · 2022Review
- Fishing for DNA? Designing baits for population genetics in target enrichment experiments: Guidelines, considerations and the new tool supeRbaits.Molecular ecology resources · 2022Article
- Development and application of the Faba_bean_130K targeted next-generation sequencing SNP genotyping platform based on transcriptome sequencing.TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik · 2021Article
- Whole-exome sequencing reveals a long-term decline in effective population size of red spruce (Evolutionary applications · 2020Article
- Article
- Selective Sweeps Lead to Evolutionary Success in an Amazonian Hyperdominant Palm.Frontiers in genetics · 2020Article
- Exome resequencing and GWAS for growth, ecophysiology, and chemical and metabolomic composition of wood of Populus trichocarpa.BMC genomics · 2019Article
- Phenotypic and Genomic Local Adaptation across Latitude and Altitude in Populus trichocarpa.Genome biology and evolution · 2019Article
- A genome-wide scan shows evidence for local adaptation in a widespread keystone Neotropical forest tree.Heredity · 2019Article
- Design and evaluation of a sequence capture system for genome-wide SNP genotyping in highly heterozygous plant genomes: a case study with a keystone Neotropical hardwood tree genome.DNA research : an international journal for rapid publication of reports on genes and genomes · 2018Article
- Article
- Dense infraspecific sampling reveals rapid and independent trajectories of plastome degradation in a heterotrophic orchid complex.The New phytologist · 2018Article
- Identification of induced mutations in hexaploid wheat genome using exome capture assay.PloS one · 2018Article
- Development of Target Sequence Capture and Estimation of Genomic Relatedness in a Mixed Oak Stand.Frontiers in plant science · 2018Article
- Liquid-phase sequence capture and targeted re-sequencing revealed novel polymorphisms in tomato genes belonging to the MEP carotenoid pathway.Scientific reports · 2017Article
- Exploiting the great potential of Sequence Capture data by a new tool, SUPER-CAP.DNA research : an international journal for rapid publication of reports on genes and genomes · 2017Article
- From Genomes to GENE-omes: Exome Sequencing Concept and Applications in Crop Improvement.Frontiers in plant science · 2017Review
- Sequence capture by hybridization to explore modern and ancient genomic diversity in model and nonmodel organisms.Nucleic acids research · 2016Review
Corrections and comments
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Authors and funding
2 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundHigh-throughput re-sequencing is rapidly becoming the method of choice for studies of neutral and adaptive processes in natural populations across taxa. As re-sequencing the genome of large numbers of samples is still cost-prohibitive in many cases, methods for genome complexity reduction have been developed in attempts to capture most ecologically-relevant genetic variation. One of these approaches is sequence capture, in which oligonucleotide baits specific to genomic regions of interest are synthesized and used to retrieve and sequence those regions.
resultsWe used sequence capture to re-sequence most predicted exons, their upstream regulatory regions, as well as numerous random genomic intervals in a panel of 48 genotypes of the angiosperm tree Populus trichocarpa (black cottonwood, or 'poplar'). A total of 20.76Mb (5%) of the poplar genome was targeted, corresponding to 173,040 baits. With 12 indexed samples run in each of four lanes on an Illumina HiSeq instrument (2x100 paired-end), 86.8% of the bait regions were on average sequenced at a depth ≥10X. Few off-target regions (>250bp away from any bait) were present in the data, but on average ~80bp on either side of the baits were captured and sequenced to an acceptable depth (≥10X) to call heterozygous SNPs. Nucleotide diversity estimates within and adjacent to protein-coding genes were similar to those previously reported in Populus spp., while intergenic regions had higher values consistent with a relaxation of selection.
conclusionsOur results illustrate the efficiency and utility of sequence capture for re-sequencing highly heterozygous tree genomes, and suggest design considerations to optimize the use of baits in future studies.
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