Previous releases of the Ornithorhynchus anatinus genome have seen the data assembled into supercontigs, in this release some of the supercontigs have been assembled into ultracontigs and chromosomes.
A few example data points :
The platypus (Ornithorhynchus anatinus) genome of a female nicknamed
"Glennie" (collected at the Upper Barnard River on Glen Rock Station,
New South Wales) was sequenced to a total of 6x whole genome coverage.
The sequencing strategy we utilized, combined whole genome shotgun
plasmid, fosmid and BAC end sequences. The combined sequence reads were
assembled using the PCAP software (Genome Res. 13(9):2164-70 2003). This
draft sequence assembly submitted to Genbank is referred to as
Ornithorhynchus_anatinus-5.0. The database now contains the longer range
mapping of the sequence onto Ultracontigs and Chromosomes. Although some
of the Supercontigs are mapped to chromosomes, these only
represent 21% of the platypus DNA, so we have not emphasised a
chromosomal view of platypus for the current release.Future improvements
to the platypus draft sequence assembly will be dependent on the
availability of funding and improvements to existing assembler software.
Funding for the sequencing of the platypus genome was provided by the
National Human Genome Research Institute (NHGRI), National Institutes of
Health (NIH).
Credits and assembly statistics
The gene set for Platypus was built using a modified version of the standard Ensembl genebuild pipeline, using available cDNA evidence to add UTRs and improve the protein-based gene models. However, this initial geneset was limited by the lack of species-specific evidence. The gene models were assessed by generating sets of potential orthologs to genes from other mammalian species and chicken. Potentially missing predictions and partial gene predictions were identified by examining the orthologs, and exonerate was to align orthologous human and chicken peptides in order to build new gene models. We have now extended the initial gene set using recently released cDNA data from 454 sequencing, plus additional annotation from the Oxford Functional Genomics group. These data have enabled us both to clarify existing models and to add additional transcripts.
The multiple alignments are being extended with new species and 2X genomes.
Read more...
Canonical transcripts have been defined for all genes in the core databases.
Read more...
| Assembly: | Ornithorhynchus_anatinus-5.0, Dec 2005 |
| Genebuild: | Ensembl, Jan 2007 |
| Database version: | 50.1g |
| Known protein-coding genes: | 54 |
| Projected protein-coding genes: | 11,147 |
| Novel protein-coding genes: | 6,750 |
| Pseudogenes: | 547 |
| RNA genes: | 3,216 |
| Genscan gene predictions: | 133,723 |
| Gene exons: | 179,340 |
| Gene transcripts: | 26,009 |
| SNPs: | 1,207,507 |
| Base Pairs: | 1,917,748,604 |
| Golden Path Length: | 2,073,148,626 |
| Most common InterPro domains: | Top 40 Top 500 |
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