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Non PCR-amplified Transcripts and AFLP fragments as reduced representations of the quail genome for 454 Titanium sequencing
BACKGROUND: SNP (Single Nucleotide Polymorphism) discovery is now routinely performed using high-throughput sequencing of reduced representation libraries. Our objective was to adapt 454 GS FLX based sequencing methodologies in order to obtain the largest possible dataset from two reduced representa...
Autores principales: | , , , , , , , , , , , , |
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Formato: | Texto |
Lenguaje: | English |
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BioMed Central
2010
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2919564/ https://www.ncbi.nlm.nih.gov/pubmed/20667075 http://dx.doi.org/10.1186/1756-0500-3-214 |
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author | Leroux, Sophie Feve, Katia Vignoles, Florence Bouchez, Olivier Klopp, Christophe Noirot, Céline Gourichon, David Richard, Sabine Leterrier, Christine Beaumont, Catherine Minvielle, Francis Vignal, Alain Pitel, Frédérique |
author_facet | Leroux, Sophie Feve, Katia Vignoles, Florence Bouchez, Olivier Klopp, Christophe Noirot, Céline Gourichon, David Richard, Sabine Leterrier, Christine Beaumont, Catherine Minvielle, Francis Vignal, Alain Pitel, Frédérique |
author_sort | Leroux, Sophie |
collection | PubMed |
description | BACKGROUND: SNP (Single Nucleotide Polymorphism) discovery is now routinely performed using high-throughput sequencing of reduced representation libraries. Our objective was to adapt 454 GS FLX based sequencing methodologies in order to obtain the largest possible dataset from two reduced representations libraries, produced by AFLP (Amplified Fragment Length Polymorphism) for genomic DNA, and EST (Expressed Sequence Tag) for the transcribed fraction of the genome. FINDINGS: The expressed fraction was obtained by preparing cDNA libraries without PCR amplification from quail embryo and brain. To optimize the information content for SNP analyses, libraries were prepared from individuals selected in three quail lines and each individual in the AFLP library was tagged. Sequencing runs produced 399,189 sequence reads from cDNA and 373,484 from genomic fragments, covering close to 250 Mb of sequence in total. CONCLUSIONS: Both methods used to obtain reduced representations for high-throughput sequencing were successful after several improvements. The protocols may be used for several sequencing applications, such as de novo sequencing, tagged PCR fragments or long fragment sequencing of cDNA. |
format | Text |
id | pubmed-2919564 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2010 |
publisher | BioMed Central |
record_format | MEDLINE/PubMed |
spelling | pubmed-29195642010-08-11 Non PCR-amplified Transcripts and AFLP fragments as reduced representations of the quail genome for 454 Titanium sequencing Leroux, Sophie Feve, Katia Vignoles, Florence Bouchez, Olivier Klopp, Christophe Noirot, Céline Gourichon, David Richard, Sabine Leterrier, Christine Beaumont, Catherine Minvielle, Francis Vignal, Alain Pitel, Frédérique BMC Res Notes Technical Note BACKGROUND: SNP (Single Nucleotide Polymorphism) discovery is now routinely performed using high-throughput sequencing of reduced representation libraries. Our objective was to adapt 454 GS FLX based sequencing methodologies in order to obtain the largest possible dataset from two reduced representations libraries, produced by AFLP (Amplified Fragment Length Polymorphism) for genomic DNA, and EST (Expressed Sequence Tag) for the transcribed fraction of the genome. FINDINGS: The expressed fraction was obtained by preparing cDNA libraries without PCR amplification from quail embryo and brain. To optimize the information content for SNP analyses, libraries were prepared from individuals selected in three quail lines and each individual in the AFLP library was tagged. Sequencing runs produced 399,189 sequence reads from cDNA and 373,484 from genomic fragments, covering close to 250 Mb of sequence in total. CONCLUSIONS: Both methods used to obtain reduced representations for high-throughput sequencing were successful after several improvements. The protocols may be used for several sequencing applications, such as de novo sequencing, tagged PCR fragments or long fragment sequencing of cDNA. BioMed Central 2010-07-28 /pmc/articles/PMC2919564/ /pubmed/20667075 http://dx.doi.org/10.1186/1756-0500-3-214 Text en Copyright ©2010 Pitel 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 | Technical Note Leroux, Sophie Feve, Katia Vignoles, Florence Bouchez, Olivier Klopp, Christophe Noirot, Céline Gourichon, David Richard, Sabine Leterrier, Christine Beaumont, Catherine Minvielle, Francis Vignal, Alain Pitel, Frédérique Non PCR-amplified Transcripts and AFLP fragments as reduced representations of the quail genome for 454 Titanium sequencing |
title | Non PCR-amplified Transcripts and AFLP fragments as reduced representations of the quail genome for 454 Titanium sequencing |
title_full | Non PCR-amplified Transcripts and AFLP fragments as reduced representations of the quail genome for 454 Titanium sequencing |
title_fullStr | Non PCR-amplified Transcripts and AFLP fragments as reduced representations of the quail genome for 454 Titanium sequencing |
title_full_unstemmed | Non PCR-amplified Transcripts and AFLP fragments as reduced representations of the quail genome for 454 Titanium sequencing |
title_short | Non PCR-amplified Transcripts and AFLP fragments as reduced representations of the quail genome for 454 Titanium sequencing |
title_sort | non pcr-amplified transcripts and aflp fragments as reduced representations of the quail genome for 454 titanium sequencing |
topic | Technical Note |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2919564/ https://www.ncbi.nlm.nih.gov/pubmed/20667075 http://dx.doi.org/10.1186/1756-0500-3-214 |
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