Macaque assembly and gene annotation

Assembly

The Mmul_10 assembly was submitted by The Genome Institute at Washington University School of Medicine on March 2019. The assembly is on chromosome level, consisting of 3,182 contigs assembled into 2,979 scaffolds. From these sequences, 22 chromosomes have been built. 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 46,608,966 while the scaffold N50 is 82,346,004.

Other assemblies

• MMUL_1 (Ensembl release 80)

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.

• Detailed information on macaque genebuild (PDF)

More information

General information about this species can be found in Wikipedia.