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

Lee BY, Howe AE, Conte MA, D'Cotta H, Pepey E, Baroiller JF, di Palma F, Carleton KL, Kocher TD - BMC Genomics (2010)

Bottom Line: 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.These sequences are an important resource for studies of gene expression, comparative mapping and annotation of the forthcoming tilapia genome sequence.

View Article: PubMed Central - HTML - PubMed

Affiliation: Department of Biology, University of Maryland, College Park, Maryland 20742, USA.

ABSTRACT

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.

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Related in: MedlinePlus

A single high density filter of retinal cDNA libraries hybridized with a rhodopsin probe. The left side of the filter contains ~9,000 clones from an un-normalized library. The right half of the filter contains ~9,000 clones from the normalized library. Normalization has greatly reduced the redundancy of the library.
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Figure 1: A single high density filter of retinal cDNA libraries hybridized with a rhodopsin probe. The left side of the filter contains ~9,000 clones from an un-normalized library. The right half of the filter contains ~9,000 clones from the normalized library. Normalization has greatly reduced the redundancy of the library.

Mentions: The normalization procedure was highly effective. Figure 1 presents Southern blots for non-normalized and normalized retinal libraries probed for rhodopsin. Each panel contains approximately 9,000 clones. The non-normalized panel shows approximately 360 clones positive for rhodopsin. The normalized panel shows only about 9 positive clones. For this gene then, the number of duplicate clones has been reduced approximately 40-fold.


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

Lee BY, Howe AE, Conte MA, D'Cotta H, Pepey E, Baroiller JF, di Palma F, Carleton KL, Kocher TD - BMC Genomics (2010)

A single high density filter of retinal cDNA libraries hybridized with a rhodopsin probe. The left side of the filter contains ~9,000 clones from an un-normalized library. The right half of the filter contains ~9,000 clones from the normalized library. Normalization has greatly reduced the redundancy of the library.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC2874815&req=5

Figure 1: A single high density filter of retinal cDNA libraries hybridized with a rhodopsin probe. The left side of the filter contains ~9,000 clones from an un-normalized library. The right half of the filter contains ~9,000 clones from the normalized library. Normalization has greatly reduced the redundancy of the library.
Mentions: The normalization procedure was highly effective. Figure 1 presents Southern blots for non-normalized and normalized retinal libraries probed for rhodopsin. Each panel contains approximately 9,000 clones. The non-normalized panel shows approximately 360 clones positive for rhodopsin. The normalized panel shows only about 9 positive clones. For this gene then, the number of duplicate clones has been reduced approximately 40-fold.

Bottom Line: 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.These sequences are an important resource for studies of gene expression, comparative mapping and annotation of the forthcoming tilapia genome sequence.

View Article: PubMed Central - HTML - PubMed

Affiliation: Department of Biology, University of Maryland, College Park, Maryland 20742, USA.

ABSTRACT

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.

Show MeSH
Related in: MedlinePlus