About the project

The Tribolium castaneum genome project has been a tremendous success and is published in Nature, two companion journal issues (IBMB and DGE) and numerous other publications listed below.

The red flour beetle, Tribolium castaneum, 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, allowing the creation of linearized chromosome sequence files. Additional mapping of the remaining unmapped sequences is on-going 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 HGSC would like to thank the many members of the Tribolium community whose hard work has made this an incredibly successful project.

Access to the data

Genome Assembly

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. 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 is now available on the ftp site containing these missing sequences. The blast databases have also been updated to reflect this change. All other data is correct, and not affected by this change.

Tribolium gene models (protein sequences) are available via the ftp site.

BLAST Searches

HGSC

• Linearized chromosome and unplaced scaffold sequences
• Assembled contigs
• Bin0 unassembled reads and Repeat reads

Traces are available from the NCBITrace Archive, which can be searched using NCBI MegaBLAST with a same species or cross species query.

White Paper

Resources

BeetleBase

NCBI Taxonomy Browser

International Genome Consortium Database

Citations

Tribolium Genome Sequencing Consortium. The genome of the model beetle and pest Tribolium castaneum. Nature 452, 949-955 (24 April 2008)

special issue Tribolium castaneum (10 articles). Development, Genes and Evolution 218 (April 2008).

Special Issue on the Tribolium Genome (11 articles). Insect Biochemistry and Molecular Biology Volume 38 Issue 4 Pages 377-498 (April 2008).

Altincicek, B., Knorr, E., and Vilcinskas, A. Beetle immunity: Identification of immune-inducible genes from the model insect Tribolium castaneum. Dev Comp Immunol 32, 585-595 (2008).

Hauser, F., Cazzamali, G., Williamson, M., Park, Y., Li, B., Tanaka, Y., Predel, R., Neupert, S., Schachtner, J., Verleyen, P., and Grimmelikhuijzen, C. J. A genome-wide inventory of neurohormone GPCRs in the red flour beetle Tribolium castaneum. Front Neuroendocrinol 29, 142-165 (2008).

Jackowska, M., Bao, R., Liu, Z., McDonald, E. C., Cook, T. A., and Friedrich, M. Genomic and gene regulatory signatures of cryptozoic adaptation: Loss of blue sensitive photoreceptors through expansion of long wavelength-opsin expression in the red flour beetle Tribolium castaneum. Front Zool 4, 24 (2007).

Konopova, B., and Jindra, M. Broad-Complex acts downstream of Met in juvenile hormone signaling to coordinate primitive holometabolan metamorphosis. Development 135, 559-568 (2008).

Li, B., Predel, R., Neupert, S., Hauser, F., Tanaka, Y., Cazzamali, G., Williamson, M., Arakane, Y., Verleyen, P., Schoofs, L., et al. Genomics, transcriptomics, and peptidomics of neuropeptides and protein hormones in the red flour beetle Tribolium castaneum. Genome Res 18, 113-122 (2008).

Marques-Souza, H., Aranda, M., and Tautz, D. Delimiting the conserved features of hunchback function for the trunk organization of insects. Development 135, 881-888 (2008).

Nunes da Fonseca, R., von Levetzow, C., Kalscheuer, P., Basal, A., van der Zee, M., and Roth, S. Self-regulatory circuits in dorsoventral axis formation of the short-germ beetle Tribolium castaneum. Dev Cell 14, 605-615 (2008).

Schinko, J. B., Kreuzer, N., Offen, N., Posnien, N., Wimmer, E. A., and Bucher, G. Divergent functions of orthodenticle, empty spiracles and buttonhead in early head patterning of the beetle Tribolium castaneum (Coleoptera). Dev Biol. (2008).

Stafflinger, E., Hansen, K. K., Hauser, F., Schneider, M., Cazzamali, G., Williamson, M., and Grimmelikhuijzen, C. J. Cloning and identification of an oxytocin/vasopressin-like receptor and its ligand from insects.. Proc Natl Acad Sci USA 105, 3262-3267 (2008).

Wang, S., Lorenzen, M. D., Beeman, R. W., and Brown, S. J Analysis of repetitive DNA distribution patterns in the Tribolium castaneum genome. Genome Biol 9, R61 (2008).

Wyder, S., Kriventseva, E. V., Schroder, R., Kadowaki, T., and Zdobnov, E. M. Quantification of ortholog losses in insects and vertebrates. Genome Biol 8, R242 (2007).

Zhu, Q., Arakane, Y., Beeman, R. W., Kramer, K. J., and Muthukrishnan, S. Functional specialization among insect chitinase family genes revealed by RNA interference. Proc Natl Acad Sci USA (2008).

Zou, Z., Evans, J. D., Lu, Z., Zhao, P., Williams, M., Sumathipala, N., Hetru, C., Hultmark, D., and Jiang, H. Comparative genomic analysis of the Tribolium immune system. Genome Biol 8, R177 (2007).