Analysis of transcriptome data in the red flour beetle, Tribolium castaneum

The whole genome sequence of Tribolium castaneum, a worldwide coleopteran pest of stored products, has recently been determined. In order to facilitate accurate annotation and detailed functional analysis of this genome, we have compiled and analyzed all available expressed sequence tag (EST) data....

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Bibliographic Details
Published in:Insect biochemistry and molecular biology 2008-04, Vol.38 (4), p.380-386
Main Authors: Park, Yoonseong, Aikins, Jamie, Wang, L.J., Beeman, Richard W., Oppert, Brenda, Lord, Jeffrey C., Brown, Susan J., Lorenzen, Marcé D., Richards, Stephen, Weinstock, George M., Gibbs, Richard A.
Format: Article
Language:English
Subjects:
algorithms
Animals
cDNA libraries
Coleoptera
Databases, Nucleic Acid
EST
Expressed Sequence Tags
Gene Expression Profiling
Gene Library
Gene model
gene models
genes
GLEAN
GLEAN model
nucleotide sequences
transcription (genetics)
transcriptome
transcriptomics
Tribolium - genetics
Tribolium - metabolism
Tribolium castaneum
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Summary:The whole genome sequence of Tribolium castaneum, a worldwide coleopteran pest of stored products, has recently been determined. In order to facilitate accurate annotation and detailed functional analysis of this genome, we have compiled and analyzed all available expressed sequence tag (EST) data. The raw data consist of 61,228 ESTs, including 10,704 obtained from NCBI and an additional 50,524 derived from 32,544 clones generated in our laboratories. These sequences were amassed from cDNA libraries representing six different tissues or stages, namely: whole embryos, whole larvae, larval hindguts and Malpighian tubules, larval fat bodies and carcasses, adult ovaries, and adult heads. Assembly of the 61,228 sequences collapsed into 12,269 clusters (groups of overlapping ESTs representing single genes), of which 10,134 mapped onto 6463 (39%) of the 16,422 GLEAN gene models (i.e. official Tribolium gene list). Approximately 1600 clusters (13% of the total) lack corresponding GLEAN models, despite high matches to the genome, suggesting that a considerable number of transcribed sequences were missed by the gene prediction programs or were removed by GLEAN. We conservatively estimate that the current EST set represents more than 7500 transcription units.
ISSN:0965-1748
1879-0240
DOI:10.1016/j.ibmb.2007.09.008