Progress 07/01/07 to 06/30/10
Outputs
Target Audience: This project filled a major gap in the genomic resources for tilapia by generating more than 116,000 ESTs for the Nile tilapia, a globally important aquaculture species. The ESTs were immediately useful to the research community studying the genetics and physiology of tilapia and related cichlid fishes. The sequences allowed the design of PCR primers for analyses of gene expression, genetic variation and genetic mapping. Many of the sequences were used in the radiation hybrid mapping of the tilapia genome by Guyon et al. 2012. The ESTs also played an important role in annotation of the first assembly of the tilapia genome by the Broad Institute (Browand et al., in review). The paper describing these ESTs (Lee et al. 2010) has already been cited more than 25 times. We expect these Sanger ESTs will continue to play an important role in training gene prediction algorithms used to annotate future assemblies of the tilapia genome. Changes/Problems: We encountered no difficulties in completing the major goals of the research as originally proposed. We exceeded the original target number of ESTs (goal 100,000, published 116,889), and our normalization procedure to remove redundant clones from the libraries was even more successful than we had hoped. We did have a secondary goal of designing a tilapia microarray. This effort was not pursued because new technologies (Illumina RNA-seq) made this microarray obsolete. What opportunities for training and professional development has the project provided? The project trained 2 postdocs and three technicians in preparation of cDNA libraries and bioinformatic analysis of the EST sequences. How have the results been disseminated to communities of interest? Our results were reported in an article published in BMC Genomics in 2010. All of the sequences have been deposited in the NCBI GenBank database. The sequences can be searched via BLAST on our www site BouillaBase.org The sequences can be viewed in the GBrowse genome viewer on our www site BouillaBase.org What do you plan to do during the next reporting period to accomplish the goals?
Nothing Reported
Impacts
What was accomplished under these goals?
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. 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. 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.
Publications
- Type:
Journal Articles
Status:
Published
Year Published:
2010
Citation:
Lee BY, Howe AE, Conte MA, D'Cotta H, Pepey E, Baroiller JF, di Palma F,
Carleton KL, Kocher TD. An EST resource for tilapia based on 17 normalized
libraries and assembly of 116,899 sequence tags. BMC Genomics. 2010 Apr
30;11:278. doi: 10.1186/1471-2164-11-278.
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