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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...

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Autores principales: 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
Formato: Texto
Lenguaje:English
Publicado: BioMed Central 2010
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.
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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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