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. The species-specific sequence resources (platypus cDNA and protein) are very limited, so the vast majority of gene models are based on genewise alignments of proteins from other species. Most of the proteins being aligned were from species genetically distant to platypus. To improve the accuracy of models generated from these proteins, the genewise alignments were made to stretches of genomic sequence rather than to 'miniseqs'. Platypus and human cDNAs were aligned and used to add UTRs to the genewise predictions where possible. 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 used to build new gene models for these based on the human and chicken ortholog peptide sequence.
There is no Ornithorhynchus anatinus-specific news this release.
Only minor changes to the database schema this release:
| Assembly: | Ornithorhynchus_anatinus-5.0, Dec 2005 |
| Genebuild: | Ensembl, May 2006 |
| Database version: | 44.1a |
| Known genes: | 50 |
| Novel genes: | 15,682 |
| Pseudogenes: | 218 |
| RNA genes: | 1,000 |
| Genscan gene predictions: | 172,113 |
| Gene exons: | 169,462 |
| Gene transcripts: | 24,981 |
| Base Pairs*: | 1,917,973,560 |
| Golden Path Length**: | 2,073,392,148 |
* Total number of base pairs = sum of lengths of DNA table
** Reference assembly (Golden path) length = sum of non-redundant top level seq regions
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