Non PCR-amplified transcripts and AFLP® fragments as reduced representations of the quail genome for 454 Titanium sequencing
2010
Leroux, Sophie | Feve, Katia | Vignoles, Florence | Bouchez, Olivier | Klopp, Christophe | Noirot, Celine | Gourichon, David | Richard, Sabine | Leterrier, Christine | Beaumont, Catherine | Minvielle, Francis | Vignal, Alain | Pitel, Frederique | Laboratoire de Génétique Cellulaire (LGC) ; Institut National de la Recherche Agronomique (INRA)-Ecole Nationale Vétérinaire de Toulouse (ENVT) ; Institut National Polytechnique (Toulouse) (Toulouse INP) ; Université de Toulouse (UT)-Université de Toulouse (UT)-Institut National Polytechnique (Toulouse) (Toulouse INP) ; Université de Toulouse (UT)-Université de Toulouse (UT) | Génopôle Toulouse Midi-Pyrénées | Unité de Biométrie et Intelligence Artificielle (ancêtre de MIAT) (UBIA) ; Institut National de la Recherche Agronomique (INRA) | Pôle d'Expérimentation Avicole de Tours (UE PEAT) ; Institut National de la Recherche Agronomique (INRA) | Institut de Génomique Fonctionnelle de Lyon (IGFL) ; École normale supérieure de Lyon (ENS de Lyon) ; Université de Lyon-Université de Lyon-Institut National de la Recherche Agronomique (INRA)-Université Claude Bernard Lyon 1 (UCBL) ; Université de Lyon-Centre National de la Recherche Scientifique (CNRS) | Physiologie de la reproduction et des comportements [Nouzilly] (PRC) ; Institut National de la Recherche Agronomique (INRA)-Institut Français du Cheval et de l'Equitation [Saumur] (IFCE)-Université de Tours (UT)-Centre National de la Recherche Scientifique (CNRS) | Unité de Recherches Avicoles (URA) ; Institut National de la Recherche Agronomique (INRA) | Génétique Animale et Biologie Intégrative (GABI) ; Institut National de la Recherche Agronomique (INRA)-AgroParisTech
Note technique Chantier qualité GA
显示更多 [+] 显示较少 [-]英语. 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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