About the project

The HGSC has sequenced the red flour beetle, Tribolium castaneum, a common pest that is also a genetic model for the Coleoptera. The version 2.0 assembly was released in September 2005. 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 70% 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).

Access to the data

Genome Assembly

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.

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.

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

Conditions for use