OfTable 1 Rhesus chromosome nomenclatureH 1 2p+ 2q3 4 5 6 7/21 8 9 10 11 12 13 14/15 20/22 16 17 18 19 X Y C 1 2a 2b 3 4 5 6 7/21 8 9 10 11 12 13 14/15 20/22 16 17 18 19 X Y G 1 2a 2b 3 4 5 6 7/21 8 9 10 11 12 13 14/15 20/22 16 17 18 19 X Y O 1 2a 2b 3 4 5 6 7/21 8 9 10 11 12 Lenvatinib 13 14/15 20/22 16 17 18 19 X Y M 1 2a 2b 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 X Y W 1 15 9 3 4 5 6 2 8 14 10 11 12 16 7 13 20 17 18 19 X Y R 1 13 12 2 5 6 4 3 8 15 9 14 11 17 7 10 20 16 18 19 X YH = Human; C = Chimpanzee; G = Gorilla; O = Orangutan; M = MacaM; W = Wienberg et al. [16]; R = Rogers et al. [17].Ion Torrent reads (which were not included in our assembly) against rheMac2, CR_1.0 and MacaM assemblies with TMAP 4.0 [18].RNA sequencing and transcript assemblyWe extracted RNA from 11 samples using standard methods and performed sequencing with an Illumina Genome Analyzer IIx. We sequenced RNA from the cerebral cortex from 6 different animals at 76 bp, (single-end reads) and deposited the sequences in the SRA under accessions [GenBank:SRX099247, SRX101205, SRX101272, SRX101273, SRX101274 and SRX101275]. We sequenced RNA from the caudate nucleus of one animal at 76 bp (paired-end reads) and deposited the sequences at SRA under accession [GenBank:SRX103458]. We sequenced RNA from the caudate nucleus, cerebral cortex, thymus, and testis from a single rhesus macaque, 001T-NHP, at 76 bp for the caudate nucleus and at 100 bp for the other tissues (paired-end reads for all samples) and deposited the sequences in the SRA under the accessions [GenBank:SRX101672, SRX092157, SRX092159 and SRX092158], respectively.To filter out genomic contamination, we aligned reads against human RefSeq mRNA transcripts using BLASTn [10]. For 76 bp reads, we filtered out sequences if they had an alignment length of 70 bp or less with human transcripts. For 100 bp reads, we filtered out sequences if they had an alignment length of 90 bp or less with human transcripts. For paired-end reads, we also removed a read if its mate was removed. We assembled filtered reads for each sample using Velvet-Oases [19,20]. We used K-mer values of PubMed ID:https://www.ncbi.nlm.nih.gov/pubmed/18111632 29 for the six samples with single reads and 31 for the remaining samples with paired-end reads. We set the coverage cutoff and expected coverage to `auto'. We set the minimum contig length to 200 bp. We used default parameters for Oases. We obtained 369,197 de novo transcripts using the Velvet/Oases pipeline. We deposited transcripts in the NCBI's Transcriptome Shotgun Assembly database under accessions [GenBank:JU319578 - JU351361; GenBank: JU470459 - JU497303; GenBank:JV043150 - JV077152; GenBank:JV451651 - JV728215] (Additional file 2). We also used reference-guided transcriptome assembly to identify rhesus transcripts. We performed spliced alignment of the rhesus RNA-seq reads to the MaSuRCA assembly using TopHat2 [21] (version 2.0.8b, default parameters). We provided the resulting BAM file of the read alignments as PubMed ID:https://www.ncbi.nlm.nih.gov/pubmed/18218841 input to Cufflinks2 [22] (version 2.02, default parameters) for reference guided transcriptome assembly. To identify rhesus orthologs of human genes, we used the BLASTx [23] program to align conceptual translations from the assembled rhesus transcripts against human reference proteins. We used the top hit in the annotation. We did not use a single set of cutoff values to identify orthologs. Instead, alignment lengths and percent similarity were manually inspected (see Annotation, procedure 1 for rationale). We identified a total of 11,.