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Koala assembly and gene annotation

The koala (Phascolarctos cinereus) is an arboreal herbivorous marsupial native to Australia. It is the only extant representative of the family Phascolarctidae and its closest living relatives are the wombats, which comprise the family Vombatidae.

Koalas typically inhabit open eucalypt woodlands, and the leaves of these trees make up most of their diet. Because this diet has limited nutritional and caloric content, koalas are largely sedentary and sleep up to 20 hours a day.

Assembly

The phaCin_unsw_v4.1 assembly was submitted by The Earlham Institute on April 2017. The assembly is on contig level, consisting of 1,907 contigs assembled into 1,907 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 11,587,828 while the scaffold N50 is 11,587,828.

Gene annotation

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

AssemblyphaCin_unsw_v4.1, INSDC Assembly GCA_002099425.1, Apr 2017
Base Pairs3,192,581,492
Golden Path Length3,192,581,492
Annotation providerEnsembl
Annotation methodFull genebuild
Genebuild startedNov 2018
Genebuild releasedDec 2018
Genebuild last updated/patchedApr 2019
Database version100.41

Gene counts

Coding genes19,833
Non coding genes5,133
Small non coding genes1,369
Long non coding genes2,993
Misc non coding genes771
Pseudogenes511
Gene transcripts45,693

Other

Genscan gene predictions45,447

About this species

HASH(0x2299c658)