Non PCR-amplified Transcripts and AFLP fragments as reduced representations of the quail genome for 454 Titanium sequencing
<p>Abstract</p> <p>Background</p> <p>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 t...
| Main Authors: | , , , , , , , , , , , , |
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| Format: | Article |
| Language: | English |
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BMC
2010-07-01
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| Series: | BMC Research Notes |
| Online Access: | http://www.biomedcentral.com/1756-0500/3/214 |
| _version_ | 1818806558663901184 |
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| author | Leterrier Christine Richard Sabine Gourichon David Noirot Céline Klopp Christophe Bouchez Olivier Vignoles Florence Feve Katia Leroux Sophie Beaumont Catherine Minvielle Francis Vignal Alain Pitel Frédérique |
| author_facet | Leterrier Christine Richard Sabine Gourichon David Noirot Céline Klopp Christophe Bouchez Olivier Vignoles Florence Feve Katia Leroux Sophie Beaumont Catherine Minvielle Francis Vignal Alain Pitel Frédérique |
| author_sort | Leterrier Christine |
| collection | DOAJ |
| description | <p>Abstract</p> <p>Background</p> <p>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.</p> <p>Findings</p> <p>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.</p> <p>Conclusions</p> <p>Both methods used to obtain reduced representations for high-throughput sequencing were successful after several improvements.</p> <p>The protocols may be used for several sequencing applications, such as <it>de novo </it>sequencing, tagged PCR fragments or long fragment sequencing of cDNA.</p> |
| first_indexed | 2024-12-18T19:11:41Z |
| format | Article |
| id | doaj.art-0220a014948849cd976d8c04a7eabcaa |
| institution | Directory Open Access Journal |
| issn | 1756-0500 |
| language | English |
| last_indexed | 2024-12-18T19:11:41Z |
| publishDate | 2010-07-01 |
| publisher | BMC |
| record_format | Article |
| series | BMC Research Notes |
| spelling | doaj.art-0220a014948849cd976d8c04a7eabcaa2022-12-21T20:56:13ZengBMCBMC Research Notes1756-05002010-07-013121410.1186/1756-0500-3-214Non PCR-amplified Transcripts and AFLP fragments as reduced representations of the quail genome for 454 Titanium sequencingLeterrier ChristineRichard SabineGourichon DavidNoirot CélineKlopp ChristopheBouchez OlivierVignoles FlorenceFeve KatiaLeroux SophieBeaumont CatherineMinvielle FrancisVignal AlainPitel Frédérique<p>Abstract</p> <p>Background</p> <p>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.</p> <p>Findings</p> <p>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.</p> <p>Conclusions</p> <p>Both methods used to obtain reduced representations for high-throughput sequencing were successful after several improvements.</p> <p>The protocols may be used for several sequencing applications, such as <it>de novo </it>sequencing, tagged PCR fragments or long fragment sequencing of cDNA.</p>http://www.biomedcentral.com/1756-0500/3/214 |
| spellingShingle | Leterrier Christine Richard Sabine Gourichon David Noirot Céline Klopp Christophe Bouchez Olivier Vignoles Florence Feve Katia Leroux Sophie 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 BMC Research Notes |
| 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 |
| url | http://www.biomedcentral.com/1756-0500/3/214 |
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