Olive baboon assembly and gene annotation

Assembly

The second assembly of the olive baboon (Papio anubis) genome was provided by the Baylor College of Medicine in June 2012. The assembly has 20 autosomal chromosomes numbered 1-20 and a sex chromosome labelled X. The assembly contains a total sequence length of 2.95Gb with 55.1Mb of gaps. There are 72,500 scaffolds (63,229 unplaced) comprised of 198,931 contigs with a scaffold N50 of 528.9Kb and a contig N50 of 40.2Kb. The N50 size is the length such that 50% of the assembled genome lies in blocks of the N50 size or longer.

The genome assembly represented here corresponds to GenBank Assembly ID GCA_000264685.1

Gene annotation

The olive baboon assembly was annotated using a standard Ensembl gene annotation system, incorporating RNAseq data provided through a collaboration between the Nonhuman Primate Reference Transcriptome Resource and the Human Genome Sequencing Center, Baylor College of Medicine.

RNASeq data set

In addition to the Ensembl gene set, we produced RNASeq-based gene models and an indexed BAM file for each of the fourteen tissue samples used by the RNASeq pipeline and also for the merged data from all tissues. Each RNASeq-based gene model represents only the best supported transcript model. We did a BLASTp of these transcript models against UniProt proteins of protein existence level 1 and 2 in order to annotate the open reading frame. The best BLAST hit is displayed as a transcript supporting evidence.

A total of 13548 gene models in the Ensembl gene set include RNAseq data as supporting evidence. Of these 13548 gene models, 8520 are annotated exclusively from RNASeq data, with a further 5028 gene models annotated using a combination of RNASeq data and other protein evidence. The RNASeq data were used to add UTR to protein coding models.

The tissue-specific sets of transcript models built using our RNAseq pipeline are as follows:

TissueNumber of gene models
bone marrow9323
cerebellum10947
colon 10690
frontal cortex12074
heart 10056
kidney10682
liver 9642
lung11123
lymph node10280
merged18190
pituitary11090
skeletal9530
spleen11163
temporal lobe12058
thymus12796

Additional splice junctions (introns) may have been identified by our pipeline and not included in the best supported transcript model. We therefore provide users with the full set of introns identified by our RNAseq pipeline to enable further analysis. These introns were identified by searching for reads that splice when mapped to the genome.

More information

General information about this species can be found in Wikipedia.

Statistics

Summary

AssemblyPapAnu2.0, INSDC Assembly GCA_000264685.1, Mar 2012
Base Pairs2,893,270,787
Golden Path Length2,948,397,226
Annotation providerEnsembl
Annotation methodFull genebuild
Genebuild startedJan 2013
Genebuild releasedJul 2014
Genebuild last updated/patchedJan 2016
Database version90.2

Gene counts

Coding genes19,210
Non coding genes9,272
Small non coding genes5,888
Long non coding genes1,669
Misc non coding genes1,715
Pseudogenes720
Gene transcripts31,109

Other

Genscan gene predictions49,256

About this species