NCBI News: Spring 2003 | Rat Genome Assembly

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Rat Genome Assembly Deposited into GenBank

With the recent deposit of the draft rat genome assembly into GenBank, researchers can view the rat genome in Entrez and from the Rat Genome Map Viewer. Other resources such as Rat Genomic BLAST and downloadable files of predicted gene and protein sequences complement the navigational and display capabilities of the Viewer.

The Whole Genome Shotgun (WGS) effort that produced the rat genome was managed by the Rat Genome Sequencing Consortium (RGSC), which is led by the Baylor College of Medicine Human Genome Sequencing Center. The current assembly is comprised of over 157,000 WGS contigs fused to produce almost 1,800 supercontigs, or scaffolds.

The rat WGS contigs are assigned accession numbers of the format “AABR########”, with the first two digits describing the project version number. Thus, the first version has the accession AABR01000000, and consists of sequences AABR01000001 through AABR01157561. One can either search for AABR01000000 in Entrez, and from its record, click to view the records AABR01000001 through AABR01157561; or, one can search for any of the individual records separately.

The WGS reads are found in the Trace Archive and can also be queried using the BLAST service described below. There are over 38,000,000 rat traces available via the “Hot Spots” “Trace archive” link on the NCBI Home Page.

More information on the assembly and other rat genomic resources is available from the NCBI “Genomic Biology” page. Follow the “Rat” link under “Organism-Specific Resources”. To download sequence and annotations via FTP, use

ftp.ncbi.nih.gov/genomes

The genome assembly can be displayed using the Rat Genome Map Viewer, as in Figure 1. In the figure, several different maps are shown, including gene sequence, component, contig, GenomeScan, UniGene, and STS. The component map shows the tiling path of the WGS contig accessions used to build the “NW_xxxxxx” scaffolds, whereas the contig map displays the placement of the scaffolds on the chromosomes. Genes that have also been annotated on the genome assembly using the alignment of mRNAs to the contigs are shown on the Genes_seq map, while GenomeScan predictions are included on a separate map. In addition, the Transcript map shows the combinations of exons, or splice variants, that are implied by mRNA alignments. The Rn_UniGene map shows the alignment of rat ESTs to the genome assembly and shows EST-only gene models based on shared introns and alignment to a common position on the genome. The STS map displays the placement, via Electronic PCR, of STSs onto the genomic scaffolds.

Try the rat MapViewer at:

www.ncbi.nlm.nih.gov/mapview

Researchers can also BLAST a query sequence against WGS contigs, WGS traces from the Trace Archive, BAC ends, HTG, RNA, and EST sequences, using the Rat Genome BLAST service. BLAST hits are shown marked in red on the genome assembly. Figure 2 shows the BLAST hit of a Bos taurus p53 tumor suppressor phosphoprotein (TP53), mRNA against the Rat genome assembly. The query sequence shows an 82% homology to the rat contig NW_042660.1. The parallel gene sequence map shows the annotated rat gene TP53 that is annotated within the same region, suggesting a homologous relationship between the Bos taurus and rat genes.

The Rat BLAST service can be accessed from the BLAST Home Page.

Click on image to view larger

Figure 1: Map Viewer display of rat genome assembly for chromosome 17 showing several parallel maps, including those for predicted and confirmed genes, and the contigs and their components. Click on “Maps and Options” to view all the available maps.

Click on image to view larger

Figure 2: BLAST hit of a Bos taurus p53 tumor suppressor phosphoprotein (TP53), mRNA against the Rat genome assembly shown in its genomic context within the MapViewer.