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Targeted enrichment of the black cottonwood (Populus trichocarpa) gene space using sequence capture

BACKGROUND: High-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 reductio...

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Autores principales: Zhou, Lecong, Holliday, Jason A
Formato: Online Artículo Texto
Lenguaje:English
Publicado: BioMed Central 2012
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3542275/
https://www.ncbi.nlm.nih.gov/pubmed/23241106
http://dx.doi.org/10.1186/1471-2164-13-703
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author Zhou, Lecong
Holliday, Jason A
author_facet Zhou, Lecong
Holliday, Jason A
author_sort Zhou, Lecong
collection PubMed
description BACKGROUND: High-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. RESULTS: We 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. CONCLUSIONS: Our 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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spelling pubmed-35422752013-01-11 Targeted enrichment of the black cottonwood (Populus trichocarpa) gene space using sequence capture Zhou, Lecong Holliday, Jason A BMC Genomics Research Article BACKGROUND: High-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. RESULTS: We 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. CONCLUSIONS: Our 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. BioMed Central 2012-12-14 /pmc/articles/PMC3542275/ /pubmed/23241106 http://dx.doi.org/10.1186/1471-2164-13-703 Text en Copyright ©2012 Zhou and Holliday; licensee BioMed Central Ltd. http://creativecommons.org/licenses/by/2.0 This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.
spellingShingle Research Article
Zhou, Lecong
Holliday, Jason A
Targeted enrichment of the black cottonwood (Populus trichocarpa) gene space using sequence capture
title Targeted enrichment of the black cottonwood (Populus trichocarpa) gene space using sequence capture
title_full Targeted enrichment of the black cottonwood (Populus trichocarpa) gene space using sequence capture
title_fullStr Targeted enrichment of the black cottonwood (Populus trichocarpa) gene space using sequence capture
title_full_unstemmed Targeted enrichment of the black cottonwood (Populus trichocarpa) gene space using sequence capture
title_short Targeted enrichment of the black cottonwood (Populus trichocarpa) gene space using sequence capture
title_sort targeted enrichment of the black cottonwood (populus trichocarpa) gene space using sequence capture
topic Research Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3542275/
https://www.ncbi.nlm.nih.gov/pubmed/23241106
http://dx.doi.org/10.1186/1471-2164-13-703
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