Macaque assembly and gene annotation

Assembly

The Mmul_8.0.1 assembly was submitted by the Baylor College of Medicine in 2015. The assembly is on the chromosome level, consisting of 348,493 contigs assembled into 286,262 scaffolds/22 chromosomes.

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 107,172 while the scaffold N50 is 4,193,270. This large contig and scaffold N50 has allowed for a much more complete annotation of the rhesus macaque genome that the previous annotation on Mmul_1.0.

Other assemblies

Gene annotation

The annotation for the protein -coding genes was carried out using three main techniques:

  • Rhesus macaque RNA-seq data from thirteen tissues.
  • Whole genome alignment against the human GRCh38 assembly followed by projection of GENCODE Basic protein-coding transcripts in regions of sufficient alignment conservation.
  • Splice-aware alignment of a subset of UniProt proteins to the Mmul_8.0.1 assembly.

The subset of UniProt proteins used was our 'primates basic' set. This consisted of the proteins from the following clades and protein existence (PE) levels:

  • Human PE level 1 & 2 proteins.
  • Other primates PE level 1, 2 & 3 proteins.
  • Mouse PE level 1 & 2 proteins.
  • Other mammals PE level 1 & 2 proteins.
  • Other vertebrates PE level 1 & 2 proteins.

UTRs were obtained (where possible) from the RNA-seq data and alignments of RefSeq rhesus macaque cDNAs.

Small ncRNAs were obtained using a combination of BLAST and Infernal/RNAfold.

Long intergenic ncRNAs were annotated from transcripts produced during the RNA-seq pipeline that had either a poor or no BLAST hit to any UniProt vertebrate PE12 protein. These transcripts are then scanned for evidence of protein domains. If no evidence was found the model was marked as lincRNA.

The annotation process is described in the document below.

More information

General information about this species can be found in Wikipedia.

Statistics

Summary

AssemblyMMUL 1.0, Feb 2006
Base Pairs3,093,871,206
Golden Path Length3,097,179,960
Annotation methodFull genebuild
Genebuild startedJan 2006
Genebuild releasedAug 2006
Genebuild last updated/patchedMay 2010
Database version90.10

Gene counts

Coding genes21,905
Pseudogenes1,762
Gene transcripts44,725

Other

Genscan gene predictions125,893
Short Variants3,123,522
Structural variants123

About this species