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Sequencing of a QTL-rich region of the Theobroma cacao genome using pooled BACs and the identification of trait specific candidate genes
BACKGROUND: BAC-based physical maps provide for sequencing across an entire genome or a selected sub-genomic region of biological interest. Such a region can be approached with next-generation whole-genome sequencing and assembly as if it were an independent small genome. Using the minimum tiling pa...
Autores principales: | , , , , , , , , , , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
BioMed Central
2011
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3154204/ https://www.ncbi.nlm.nih.gov/pubmed/21794110 http://dx.doi.org/10.1186/1471-2164-12-379 |
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author | Feltus, Frank A Saski, Christopher A Mockaitis, Keithanne Haiminen, Niina Parida, Laxmi Smith, Zachary Ford, James Staton, Margaret E Ficklin, Stephen P Blackmon, Barbara P Cheng, Chun-Huai Schnell, Raymond J Kuhn, David N Motamayor, Juan-Carlos |
author_facet | Feltus, Frank A Saski, Christopher A Mockaitis, Keithanne Haiminen, Niina Parida, Laxmi Smith, Zachary Ford, James Staton, Margaret E Ficklin, Stephen P Blackmon, Barbara P Cheng, Chun-Huai Schnell, Raymond J Kuhn, David N Motamayor, Juan-Carlos |
author_sort | Feltus, Frank A |
collection | PubMed |
description | BACKGROUND: BAC-based physical maps provide for sequencing across an entire genome or a selected sub-genomic region of biological interest. Such a region can be approached with next-generation whole-genome sequencing and assembly as if it were an independent small genome. Using the minimum tiling path as a guide, specific BAC clones representing the prioritized genomic interval are selected, pooled, and used to prepare a sequencing library. RESULTS: This pooled BAC approach was taken to sequence and assemble a QTL-rich region, of ~3 Mbp and represented by twenty-seven BACs, on linkage group 5 of the Theobroma cacao cv. Matina 1-6 genome. Using various mixtures of read coverages from paired-end and linear 454 libraries, multiple assemblies of varied quality were generated. Quality was assessed by comparing the assembly of 454 reads with a subset of ten BACs individually sequenced and assembled using Sanger reads. A mixture of reads optimal for assembly was identified. We found, furthermore, that a quality assembly suitable for serving as a reference genome template could be obtained even with a reduced depth of sequencing coverage. Annotation of the resulting assembly revealed several genes potentially responsible for three T. cacao traits: black pod disease resistance, bean shape index, and pod weight. CONCLUSIONS: Our results, as with other pooled BAC sequencing reports, suggest that pooling portions of a minimum tiling path derived from a BAC-based physical map is an effective method to target sub-genomic regions for sequencing. While we focused on a single QTL region, other QTL regions of importance could be similarly sequenced allowing for biological discovery to take place before a high quality whole-genome assembly is completed. |
format | Online Article Text |
id | pubmed-3154204 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2011 |
publisher | BioMed Central |
record_format | MEDLINE/PubMed |
spelling | pubmed-31542042011-08-11 Sequencing of a QTL-rich region of the Theobroma cacao genome using pooled BACs and the identification of trait specific candidate genes Feltus, Frank A Saski, Christopher A Mockaitis, Keithanne Haiminen, Niina Parida, Laxmi Smith, Zachary Ford, James Staton, Margaret E Ficklin, Stephen P Blackmon, Barbara P Cheng, Chun-Huai Schnell, Raymond J Kuhn, David N Motamayor, Juan-Carlos BMC Genomics Research Article BACKGROUND: BAC-based physical maps provide for sequencing across an entire genome or a selected sub-genomic region of biological interest. Such a region can be approached with next-generation whole-genome sequencing and assembly as if it were an independent small genome. Using the minimum tiling path as a guide, specific BAC clones representing the prioritized genomic interval are selected, pooled, and used to prepare a sequencing library. RESULTS: This pooled BAC approach was taken to sequence and assemble a QTL-rich region, of ~3 Mbp and represented by twenty-seven BACs, on linkage group 5 of the Theobroma cacao cv. Matina 1-6 genome. Using various mixtures of read coverages from paired-end and linear 454 libraries, multiple assemblies of varied quality were generated. Quality was assessed by comparing the assembly of 454 reads with a subset of ten BACs individually sequenced and assembled using Sanger reads. A mixture of reads optimal for assembly was identified. We found, furthermore, that a quality assembly suitable for serving as a reference genome template could be obtained even with a reduced depth of sequencing coverage. Annotation of the resulting assembly revealed several genes potentially responsible for three T. cacao traits: black pod disease resistance, bean shape index, and pod weight. CONCLUSIONS: Our results, as with other pooled BAC sequencing reports, suggest that pooling portions of a minimum tiling path derived from a BAC-based physical map is an effective method to target sub-genomic regions for sequencing. While we focused on a single QTL region, other QTL regions of importance could be similarly sequenced allowing for biological discovery to take place before a high quality whole-genome assembly is completed. BioMed Central 2011-07-27 /pmc/articles/PMC3154204/ /pubmed/21794110 http://dx.doi.org/10.1186/1471-2164-12-379 Text en Copyright ©2011 Feltus et al; 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 Feltus, Frank A Saski, Christopher A Mockaitis, Keithanne Haiminen, Niina Parida, Laxmi Smith, Zachary Ford, James Staton, Margaret E Ficklin, Stephen P Blackmon, Barbara P Cheng, Chun-Huai Schnell, Raymond J Kuhn, David N Motamayor, Juan-Carlos Sequencing of a QTL-rich region of the Theobroma cacao genome using pooled BACs and the identification of trait specific candidate genes |
title | Sequencing of a QTL-rich region of the Theobroma cacao genome using pooled BACs and the identification of trait specific candidate genes |
title_full | Sequencing of a QTL-rich region of the Theobroma cacao genome using pooled BACs and the identification of trait specific candidate genes |
title_fullStr | Sequencing of a QTL-rich region of the Theobroma cacao genome using pooled BACs and the identification of trait specific candidate genes |
title_full_unstemmed | Sequencing of a QTL-rich region of the Theobroma cacao genome using pooled BACs and the identification of trait specific candidate genes |
title_short | Sequencing of a QTL-rich region of the Theobroma cacao genome using pooled BACs and the identification of trait specific candidate genes |
title_sort | sequencing of a qtl-rich region of the theobroma cacao genome using pooled bacs and the identification of trait specific candidate genes |
topic | Research Article |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3154204/ https://www.ncbi.nlm.nih.gov/pubmed/21794110 http://dx.doi.org/10.1186/1471-2164-12-379 |
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