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  Construction of a 'unigene' cDNA clone set by oligonucleotide fingerprinting allows access to 25 000 potential sugar beet genes

Herwig, R., Schulz, B., Weisshaar, B., Hennig, S., Steinfath, M., Drungowski, M., et al. (2002). Construction of a 'unigene' cDNA clone set by oligonucleotide fingerprinting allows access to 25 000 potential sugar beet genes. The Plant Journal, 32(5), 845-857.

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Item Permalink: http://hdl.handle.net/11858/00-001M-0000-0010-8B71-8 Version Permalink: http://hdl.handle.net/11858/00-001M-0000-0010-8B72-6
Genre: Journal Article

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 Creators:
Herwig, Ralf1, Author              
Schulz, Britta, Author
Weisshaar, Bernd, Author
Hennig, Steffen2, Author              
Steinfath, Matthias3, Author
Drungowski, Mario3, Author
Stahl, Dietmar, Author
Wruck, Wasco3, Author
Menze, Andreas, Author
O'Brien, John, Author
Lehrach, Hans2, Author              
Radelof, Uwe2, Author              
Affiliations:
1Bioinformatics (Ralf Herwig), Dept. of Vertebrate Genomics (Head: Hans Lehrach), Max Planck Institute for Molecular Genetics, Max Planck Society, ou_1479648              
2Dept. of Vertebrate Genomics (Head: Hans Lehrach), Max Planck Institute for Molecular Genetics, Max Planck Society, ou_1433550              
3Max Planck Society, ou_persistent13              

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 Abstract: Access to the complete gene inventory of an organism is crucial to understanding physiological processes like development, differentiation, pathogenesis, or adaptation to the environment. Transcripts from many active genes are present at low copy numbers. Therefore, procedures that rely on random EST sequencing or on normalisation and subtraction methods have to produce massively redundant data to get access to low-abundance genes. Here, we present an improved oligonucleotide fingerprinting (ofp) approach to the genome of sugar beet (Beta vulgaris), a plant for which practically no molecular information has been available. To identify distinct genes and to provide a representative 'unigene' cDNA set for sugar beet, 159 936 cDNA clones were processed utilizing large-scale, high-throughput data generation and analysis methods. Data analysis yielded 30 444 ofp clusters reflecting the number of different genes in the original cDNA sample. A sample of 10 961 cDNA clones, each representing a different cluster, were selected for sequencing. Standard sequence analysis confirmed that 89% of these EST sequences did represent different genes. These results indicate that the full set of 30 444 ofp clusters represent up to 25 000 genes. We conclude that the ofp analysis pipeline is an accurate and effective way to construct large representative 'unigene' sets for any plant of interest with no requirement for prior molecular sequence data.

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Language(s): eng - English
 Dates: 2002-12
 Publication Status: Published in print
 Pages: -
 Publishing info: -
 Table of Contents: -
 Rev. Method: -
 Identifiers: eDoc: 25782
 Degree: -

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Title: The Plant Journal
Source Genre: Journal
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Pages: - Volume / Issue: 32 (5) Sequence Number: - Start / End Page: 845 - 857 Identifier: -