We have processed the RNAseq data for Indian-origin rhesus macaque and Mauritian-origin cynomolgus macaque, and generated updated genome annotations for both macaques. The work was detailed in Peng et al, 2014.. The updated annotation can be downloaded from here.
In brief, for both macaque species we uncovered thousands of novel isoforms for annotated genes and thousands of un-annotated intergenic transcripts enriched with non-coding RNAs. We also identified thousands of transcript sequences which are partially or completely ‘missing’ from current macaque genome assemblies. Many newly identified transcripts were differentially expressed during SIV infection of rhesus macaques or during Ebola virus infection of cynomolgus macaques.