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

TitleAnalysis of transcriptome data in the red flour beetle, Tribolium castaneum.
Publication TypeJournal Article
Year of Publication2008
AuthorsPark, Y, Aikins, J, Wang, LJ, Beeman, RW, Oppert, B, Lord, JC, Brown, SJ, Lorenzen, MD, Richards, S, Weinstock, GM, Gibbs, RA
JournalInsect Biochem Mol Biol
Volume38
Issue4
Pagination380-6
Date Published2008 Apr
ISSN0965-1748
KeywordsAnimals, Databases, Nucleic Acid, Expressed Sequence Tags, Gene Expression Profiling, Gene Library, Tribolium
Abstract

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 6,463 (39%) of the 16,422 GLEAN gene models (i.e. official Tribolium gene list). Approximately 1,600 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 7,500 transcription units.

DOI10.1016/j.ibmb.2007.09.008
Alternate JournalInsect Biochem. Mol. Biol.
PubMed ID18342244
PubMed Central IDPMC2387101
Grant ListP20 RR016475 / RR / NCRR NIH HHS / United States
R01 HD029594-16 / HD / NICHD NIH HHS / United States
R01 HD029594 / HD / NICHD NIH HHS / United States
P20 RR 016475 / RR / NCRR NIH HHS / United States
P20 RR016475-02 / RR / NCRR NIH HHS / United States