Red Flour Beetle Genome Project
Red flour beetle
2008 Mar 24
T. castaneum genome
About the Project
The Tribolium castaneum genome sequence and its analysis has been published in Nature, two companion journal issues (IBMB and DGE) and numerous other publications listed below.
The red flour beetle (Tribolium castaneum) is a common pest that is also a genetic model for the Coleoptera.
The genome has been sequenced to 7-fold coverage using a whole genome shotgun approach and assembled using the HGSC's assembly engine, Atlas, with methods employed for the Drosophila pseudoobscura genome assembly. Approximately 90% of the genome sequence has been mapped to chromosomes in collaboration with Dick Beeman (USDA ARS) and Sue Brown (Kansas State University).
Funding for this project has been provided by the National Human Genome Research Institute (NHGRI U54 HG003273), which is part of the National Institutes of Health (NIH), and the U.S. Department of Agriculture's Agricultural Research Service (USDA ARS Agreement No. 58-5430-3-338).
We at the BCM-HGSC would like to thank the many members of the Tribolium community whose hard work has made this a successful project.
Access to the Data
The long term home of the Tribolium genome is Beetlebase.
Tcas 3.0 is now available in GenBank and on our FTP site. Note there are no restrictions of any kind on the Tribolium data as it has been published
Version 2 of the assembly, Tcas_2.0 is available for download using the FTP Data link in the sidebar. The assembly is described in detail in the README in that directory. T.cas_1.0 was a preliminary genome assembly that did not include large insert paired end information and has been moved to a previous assemblies folder.
A genboree browser of the Tcas2.0 sequence is available here: There are also links to the genboree browser from the blast results (at the bottom of each reported HSP) if you use the blast server on this page.
The original linear scaffold file, Tcas2.0/linearScaffolds/Tcas20050914-genome, posted on the ftp site did not include singleton contigs from the assembly and thus did not fully reflect the tribolium genome sequence, missing ~4.4Mb of sequence in 1860 contigs and reptigs or approximately 2.5% of the assembled sequence. A corrected Tcas20051011-genome file containing these missing sequences is now available on the ftp site. The blast databases have also been updated to reflect this change. All other data is correct, and not affected by this change.
The BLAST link is located in the sidebar.
Linearized chromosome and unplaced scaffold sequences
Bin0 unassembled reads and Repeat reads
Traces are available from the NCBI Trace Archive by using the link in the sidebar, or by using NCBI MegaBLAST with a same species or cross species query.
Selected PubMed Citations
Tribolium Genome Sequencing Consortium, Richards, S, Gibbs, RA, Weinstock, GM, Brown, SJ, Denell, R, Beeman, RW, Gibbs, R, Beeman, RW et al. The genome of the model beetle and pest Tribolium castaneum. Nature 2008 Apr 24; 452(7190):949-55. [PubMed]
Park, Y, Aikins, J, Wang, LJ, Beeman, RW, Oppert, B, Lord, JC, Brown, SJ, Lorenzen, MD, Richards, S et al. Analysis of transcriptome data in the red flour beetle, Tribolium castaneum. Insect Biochem. Mol. Biol. 2008 Apr; 38(4):380-6. [PubMed]