PubMed Nucleotide Protein Genome Structure Taxonomy

Tribolium castaneum genome data and search tips Revised April 12, 2006

The Map Viewer help document describes in general how to use the Map Viewer software. This page describes the data available for Tribolium castaneum (the red flour beetle), and the search tips specific to that organism. You can also return to the Tribolium castaneum genome view search page. The Map Viewer home page allows you to search the genome data of any organism represented in Map Viewer.

  1. Scope of Data
  2. Available Maps
  3. Constructing Queries
  4. Constructing URLs

Scope of Data back to top

The Map Viewer provides a view of Tribolium castaneum data from a variety of sources described below.

Tribolium castaneum Genomic Sequence Data back to top

The current Tribolium castaneum genome build (1.1) is based on the Tcas_2.0 assembly provided by the Baylor College of Medicine in September 2005. The genome sequence was derived from purified nuclei of embryos of mixed sex from the inbred strain Georgia 2. The sequencing strategy, which included whole genome shotgun sequencing with some fosmid and BAC end sequencing to aid scaffolding, produced a 7.3x coverage of the Tribolium castaneum genome.

The mitochondrial sequence presented, NC_003081, is based on the work of Friedrich and Muqim (2003).

BLAST Tribolium castaneum Genomic Sequence back to top

The complete set of Tribolium castaneum sequence databases available for BLAST searching is shown in the pop-up menu on the Tribolium castaneum BLAST page, which includes a link to the database descriptions. In addition, those interested in comparative genomics may use the arthropod genomes BLAST page, which includes individual and combined sequence databases for Drosophila melanogaster, Drosophila pseudoobscura, Anopheles gambiae, Apis mellifera and others.

Additional Tribolium castaneum Genome Resources back to top

In addition to the Tribolium castaneum data available in the Map Viewer and through BLAST, links to NCBI resources and external sites are available from the Tribolium castaneum Genome Resource Guide.

Available Maps back to top

The available maps for Tribolium castaneum include:

Sequence Maps back to top

Ab initio

Shows models generated by Gnomon. mRNA alignments were used to segment the genomic sequence by putative gene boundaries, and Gnomon was executed on these segments to predict genes. Gnomon uses protein alignments in addition to transcript alignments and, in order to capture as much coding information in the genome as possible in this assembly, Gnomon models may represent partial as well as complete coding sequences. Models with a completely supported CDS are blue, models with a partially supported CDS are green, and the pure ab initio predictions are brown. Pure ab initio status indicates that the model was built without the support of mRNA or protein alignments, either through failure to align the sequence to the genome or an alignment ignored by Gnomon due to a score falling below a pre-determined threshold.

Component

Provides the tiling path of GenBank AAJJxxxxxxxx accessions from the whole genome shotgun project (AAJJ00000000.1) used to build each of the NW_xxxxxxxxx WGS contigs, which are described below.

Contig

Shows the chromosomal placement of NW_xxxxxxxxx contigs on the assembled genome sequence. Individual GenBank records used to assemble the contigs are shown on the Component map, described above.

Tca RNA Shows the alignment of individual Tribolium castaneum transcripts to the assembled genomic sequence. The corresponding alignment of EST clusters is shown in the Tca_UniG map, described below.

Dm RNA Shows the alignment of individual Drosophila melanogaster transcripts to the assembled genomic sequence. The corresponding alignment of EST clusters is shown in the Dm_UniG map, described below.

Ins RNA

Shows the alignment of individual insect transcripts to the assembled genomic sequence. The corresponding alignment of insect EST clusters is shown in the Ins_UniG map, described below.

GenBank_DNA

Shows the placement of Tribolium castaneum genomic DNA sequences from GenBank that were not used in the assembly of contigs. Placement is based on the alignment of the sequences to the components of the contigs. It includes Tribolium castaneum genomic sequences longer than 500 bp that have at least 97% identity to the components for at least 98 base pairs. If a sequence extends beyond a contig, that portion of sequence is not shown. The 'hits' link leads to a tabular display that shows the matching regions (base spans) of the assembly component and the GenBank genomic DNA record that has been aligned to it.

The length of a line represents the upper and lower-most points on the genome assembly to which sequence fragments from a single GenBank record were aligned.

When the GenBank_DNA map is displayed as the master map, in the default verbose mode, the descriptive text includes several columns: Total Bases which shows the total number of bases in the GenBank record; Aligned Bases which shows the total number of bases from that record that were aligned to the genome; % identity for the alignment; % coverage which shows how much of the Genbank record aligned to the genome as a percentage; Alignment-length ratio, which is the ratio of the alignment length in the genome to the alignment length of the Genbank record; and Strain from which the Genbank record was derived, when available.
Genes_Sequence

Shows genes that have been annotated on the genomic contigs. This includes known and putative genes placed as a result of alignments of mRNAs to the contigs.

If multiple models exist for a single gene, corresponding to splicing variants, the Gene_Sequence map presents a flattened view of all the exons that can be spliced together in various ways. For example, if one splice variant uses exons 1, 3, 4, and another splice variant uses exons 2, 3, 4, the Gene_Sequence map shows exons 1, 2, 3, 4. (In comparison, the Transcript (RNA) map shows what combinations of exons are valid based on mRNA sequences from RefSeq and GenBank.)

Genes shown on the left of the grey line are transcribed in the - orientation (from bottom up), and those on the right in the + orientation (from top down).

When Gene_Sequence is selected as the Master map, the verbose display (detailed labeling, shown by default) includes arrows to the right of each gene name indicate its direction of transcription as well as links to:

Additional information about these links is also provided in the Map Viewer Help Document, under Links to Related Resources.

Gene models are shown in five colors, depending on the type of evidence that was used to construct the models. The one or two letter code shown in the evidence column (that is displayed when Gene_Sequence is the master map) also indicates the type of evidence.

 
Gene Color Evidence Code Type of evidence used to construct gene model
Blue C Confirmed gene model - model based on alignment of mRNA, or mRNAs plus ESTs, to the genomic sequence (see additional notes, below)
Light Green E EST only - model based on EST evidence only
Dark Brown PE Predicted+EST - model predicted by Gnomon and EST evidence (more about Gnomon)
Light Brown P Predicted only - model predicted by Gnomon (more about Gnomon)
Orange ? Conflict - there is some discrepancy between the mRNA sequence and the gene model (see additional notes, below)
  I Interim LocusID - model based alignment of mRNAs, or mRNAs plus ESTs, to the genome, in which the aligning transcripts could not be unambiguously assigned to a preexisting LocusID (see additional notes, below)

  Additional Notes:

In general, a gene model is shown in blue if there is a clean alignment between a RefSeq or GenBank mRNA sequence and the genomic sequence, and if there is an exact match between the protein product that was annotated in the mRNA sequence record and the conceptual translation of the genomic sequence gene model.

A gene model is shown in orange if there is some discrepancy between the mRNA sequence and the gene model, either in the alignment of the two and/or in their protein products. Examples of the former can include gaps, or the alignment of an mRNA to two or more genomic regions. Examples of the latter can include differences between the amino acid sequence given in an mRNA sequence record and the conceptual translation of the corresponding gene model, or premature termination of a coding region in the genomic sequence. Both of those can be caused by base pair mismatches between the mRNA and genomic sequence.

Models with Interim LocusIDs (LOC######, evidence code I) may be paralogs, genes not yet curated, duplications because of assembly errors, or pseudogenes. The genome assembly and annotation pipeline assigns interim IDs when there is no unambiguous solution to what they should be. An interim LocusID is always associated with a RefSeq XM_* accession (model mRNA), although supporting alignments may (or may not) include RefSeq NM_* accessions (known mRNAs). More about RefSeq and RefSeq accessions can be found at the RefSeq homepage.

RefSeq Transcripts

Shows diagrams of the RNAs that are predicted on the genomic contigs. The Transcript map and Gene_Sequence map are built in the same way, using the same types of evidence, described above. The Gene_Sequence map, however, shows a view of all the exons in a gene, while the Transcript map shows the combinations of exons (i.e., splice variants) that are valid, based on mRNA sequences.

STS Shows the placement of STSs from a variety of sources onto the assembled genomic sequence (the NW_xxxxxxxxx contigs, described above) using Electronic-PCR (e-PCR).

Tca_UniG Shows the alignment of Tribolium castaneum EST clusters to the assembled genomic sequence. ESTs are clustered based on shared introns and alignment to a common position on the genome. Those ESTs can come from one or more UniGene clusters, whose IDs are noted by the EST cluster. (UniGene clusters are made with a different build procedure, so there is not necessarily a one-to-one correspondence between EST clusters on the Tca_UniG map and clusters in the UniGene resource.)

Dm_UniG Shows the alignment of Drosophila melanogaster EST clusters to the assembled genomic sequence. ESTs are clustered based on shared introns and alignment to a common position on the genome. Those ESTs can come from one or more UniGene clusters, whose IDs are noted by the EST cluster. (UniGene clusters are made with a different build procedure, so there is not necessarily a one-to-one correspondence between EST clusters on the Dm_UniG map and clusters in the UniGene resource.)

Ins_UniG Shows the alignment of EST clusters from other insect species to the assembled genomic sequence. ESTs are clustered based on shared introns and alignment to a common position on the genome. Those ESTs can come from one or more UniGene clusters, whose IDs are noted by the EST cluster. (UniGene clusters are made with a different build procedure, so there is not necessarily a one-to-one correspondence between EST clusters on the Ins_UniG map and clusters in the UniGene resource.)

Genetic Linkage (Meiotic) Maps back to top

Lorenzen et al. (2005) A genetic linkage with 424 markers, including a large number derived from BAC end sequences that were used to anchor the sequence map to most of the linkage groups, is described by Lorenzen et al. (2005) in "Genetic linkage maps of the red flour beetle, Tribolium castaneum, based on bacterial artificial chromosomes and expressed sequence tags. Genetics, 170:741-747.

Constructing queries back to top

Searchable Terms back to top

The Map Viewer supports searching on any term that describes an element on any map, including:

  • gene symbol
    A search for Cx will retrieve the locus cephalothorax.
  • marker name and alias
  • GenBank accession number
  • text words
    For example, a search for actin will retrieve all map objects containing that word in their description. If multiple terms are entered. they will automatically be combined with the 'AND' Boolean operator.

Map Positions back to top

As noted in the Search By Position section of the Map Viewer help document, there are three main ways to search by map position from the Map View of a chromosome:
  1. enter a range of interest in the Region text boxes in side bar
  2. click on the region of interest in the chromosome thumbnail graphic in the sidebar
  3. click on a region of interest in the enlarged Map View of the chromosome

For Tribolium castaneum, the following types of map positions can be entered in option 1:
  • symbols - you can enter marker names or alternate marker names (aliases) to display a region of the chromosome between those mapped elements. Note that both mapped elements must be present on the maps that share the same coordinate system in order for the range search to work properly.

  • numerical positions - can be used if the master map is a genetic map, radiation hybrid map, or sequence map. It is not necessary to specify units. The Map Viewer will interpret the range in the units of the master map. Note that for a sequence map, base pair positions may be entered in any of the following formats: 1000000 or 1,000,000 or 1M or 1000K.

General Tips back to top

As mentioned in the Searchable Terms section of the Map Viewer Help Document, any term entered in the query box will be treated as an independent entity to be joined by the 'AND' Boolean operator. It is also possible to construct more complex queries by using explicit Boolean operators (AND, OR, NOT), field restriction, or limiting retrieval to records that have certain properties.

The Advanced Search page allows you to use a number of query options by simply checking boxes or radio buttons that represent various search fields, properties, and object types. It also allows you to limit your query to one or more chromosomes. The Advanced Search page is accessible from the header region of the genome view page.

Constructing URLs that link to Map Viewer back to top

If you would like to create WWW links to the Map Viewer, the instructions for constructing URLs are given in the general Map Viewer Help document. You can construct URLs that either perform a search or display a specific mapped object or chromosomal region. For example:

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