An EST resource for tilapia based on 17 normalized libraries and assembly of 116,899 sequence tags

Lee Bo-Young, Howe Aimée E., Conte Matthew A., D'Cotta Helena, Pepey Elodie, Baroiller Jean-François, Di Palma Frederica, Carleton Karen L., Kocher Thomas D.. 2010. An EST resource for tilapia based on 17 normalized libraries and assembly of 116,899 sequence tags. BMC Genomics, 11:278, 10 p.

Quartile : Q1, Sujet : BIOTECHNOLOGY & APPLIED MICROBIOLOGY / Quartile : Q1, Sujet : GENETICS & HEREDITY

Résumé : Background: Large collections of expressed sequence tags (ESTs) are a fundamental resource for analysis of gene expression and annotation of genome sequences. We generated 116,899 ESTs from 17 normalized and two non-normalized cDNA libraries representing 16 tissues from tilapia, a cichlid fish widely used in aquaculture and biological research. Results: The ESTs were assembled into 20,190 contigs and 36,028 singletons for a total of 56,218 unique sequences and a total assembled length of 35,168,415 bp. Over the whole project, a unique sequence was discovered for every 2.079 sequence reads. 17,722 (31.5%) of these unique sequences had significant BLAST hits (e-value < 10-10) to the UniProt database. Conclusion: Normalization of the cDNA pools with double-stranded nuclease allowed us to efficiently sequence a large collection of ESTs. These sequences are an important resource for studies of gene expression, comparative mapping and annotation of the forthcoming tilapia genome sequence.

Mots-clés Agrovoc : tilapia (genre), séquence nucléotidique, ADN recombiné, expression des gènes, génome

Classification Agris : L10 - Génétique et amélioration des animaux
M12 - Production de l'aquaculture

Champ stratégique Cirad : Axe 1 (2005-2013) - Intensification écologique

Auteurs et affiliations

• Lee Bo-Young, University of Maryland (USA)
• Howe Aimée E., University of Maryland (USA)
• Conte Matthew A., University of Maryland (USA)
• D'Cotta Helena, CIRAD-PERSYST-UPR Aquaculture (FRA) ORCID: 0000-0003-2739-3476
• Pepey Elodie, CIRAD-PERSYST-UPR Aquaculture (FRA)
• Baroiller Jean-François, CIRAD-PERSYST-UPR Aquaculture (FRA) ORCID: 0000-0002-0992-1725
• Di Palma Frederica, Broad Institut (USA)
• Carleton Karen L., University of Maryland (USA)
• Kocher Thomas D., University of Maryland (USA)

Source : Cirad - Agritrop (https://agritrop.cirad.fr/556389/)

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