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Wallaby assembly and gene annotation

Assembly

The Meug_1.1 assembly was submitted by Tammar Wallaby Genome Sequencing Consortium on January 2010. The assembly is on scaffold level, consisting of 1,174,382 contigs assembled into 277,711 scaffolds. The N50 size is the length such that 50% of the assembled genome lies in blocks of the N50 size or longer. The N50 length for the contigs is 2,602 while the scaffold N50 is 36,602.

The genome assembly represented here corresponds to GenBank Assembly ID GCA_000004035.1

Gene annotation

The tammar wallaby (Macropus eugenii), also known as the dama wallaby or darma wallaby, is a small macropod native to South and Western Australia. Though its geographical range has been severely reduced since European colonisation, the tammar remains common within its reduced range and is listed as "Least Concern" by the International Union for Conservation of Nature (IUCN). It has been introduced to New Zealand and reintroduced to some areas of Australia where it had been previously eradicated. Skull differences distinguish tammars from Western Australia, Kangaroo Island and mainland South Australia, making them distinct population groups or possibly different subspecies.The tammar is among the smallest of the wallabies in the genus Macropus. Its coat colour is largely grey. The tammar has several notable adaptations, including the ability to retain energy while hopping, colour vision and the ability to drink seawater. A nocturnal species, it spends nighttime in grassland habitat and daytime in shrubland. It is also very gregarious and has a seasonal, promiscuous mating pattern. A female tammar can nurse a joey in her pouch while keeping an embryo in her uterus. The tammar is a model species for research on marsupials, and on mammals in general. It is one of many organisms to have had its genome sequenced.

The gene annotation process was carried out using a combination of protein-to-genome alignments, annotation mapping from a suitable reference species and RNA-seq alignments (where RNA-seq data with appropriate meta data were publicly available). For each candidate gene region, a selection process was applied to choose the most appropriate set of transcripts based on evolutionary distance, experimental evidence for the source data and quality of the alignments.
Small ncRNAs were obtained using a combination of BLAST and Infernal/RNAfold.
Pseudogenes were calculated by looking at genes with a large percentage of non-biological introns (introns of <10bp), where the gene was covered in repeats, or where the gene was single exon and evidence of a functional multi-exon paralog was found elsewhere in the genome.
lincRNAs were generated via RNA-seq data where no evidence of protein homology or protein domains could be found in the transcript.

In accordance with the Fort Lauderdale Agreement , please check the publication status of the genome/assembly before publishing any genome-wide analyses using these data.

More information

General information about this species can be found in Wikipedia.

Statistics

Summary

AssemblyMeug_1.0, INSDC Assembly GCA_000004035.1, Dec 2008
Base Pairs2,549,429,531
Golden Path Length2,955,773,937
Annotation providerEnsembl
Annotation methodProjection build
Genebuild startedFeb 2009
Genebuild releasedJun 2009
Genebuild last updated/patchedMay 2010
Database version94.1

Gene counts

Coding genes15,290
Non coding genes1,472
Small non coding genes1,430
Misc non coding genes42
Pseudogenes1,496
Gene transcripts18,310

Other

Genscan gene predictions122,304

About this species