In October 2007, the Tribolium castaneum Genome Project, led by the Human Genome Sequencing Center at the Baylor College of Medicine, released Tcas_3.0, a 7.3x coverage of the genome sequence of Tribolium castaneum. The Tribolium castaneum genome is estimated to be 158 Mb, organized as nine pairs of autosomes and one pair of sex chromosomes, X and Y. This release was produced by assembling whole genome shotgun (WGS) sequences using the Atlas genome assembly system, with BAC and fosmid end sequences used for scaffolding. The source of DNA was purified nuclei from embryos of mixed sex from the highly inbred strain Georgia 2. The use of DNA from both sexes resulted in the X and Y chromosomes being represented 75% and 25%, respectively, relative to the autosomes. More than 70% of the scaffolds have been anchored to the genetic map of Lorenzen et al. 2005, on which the numbering of linkage groups is based, however, none of the contigs has been placed on a chromosome. No linkage data for the Y chromosome is currently available due to the nature of the mapping population used.
The NCBI Map Viewer provides graphical displays of features on the genome sequence assembly. Map features that can be seen along the sequence include NCBI contigs (the 'Contig' map), the WGS sequences (the 'Component' map), and the location of genes, STSs, ESTs, and Gnomon predicted gene models. Further documentation is provided to describe the resource features and methods used, tutorials, and statistics.
You can find genes or markers of interest by submitting a query against the whole genome or one linkage group at a time. Results are indicated both graphically, as tick marks on the linkage group diagrams, or in a tabular format. The results table includes links to a chromosome graphical view where the gene or marker can be seen in the context of additional data. For genes, a particularly useful display includes the Gene, Ab initio (i.e. the Gnomon predicted gene models), and rnaTca (i.e. Tribolium castaneum ESTs and mRNAs) sequence maps. Use the "Maps & Options" window to configure each display.
The NCBI Map Viewer also presents a graphical view of the genetic map of Lorenzen et al. 2005, and includes additional markers mapped after the original publication. Each marker on the genetic map is linked to NCBI's UniSTS resource, which provides regular updates on positioning of these markers on sequences available in DDBJ/EMBL/GenBank. Navigation from these markers to information in Gene, GenBank, RefSeq, HomoloGene, and UniGene is possible.
Other genomes can also be viewed in the NCBI Map Viewer. The
Map Viewer home page provides a current list. Also consider reviewing the resources listed on the
Genomic Biology site.
Available Documentation:
Last modified: Jun 12 2008
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