Ds to the rheMac2, CR_1.0 and MacaM assemblies, respectively. This suggests

Ds to the rheMac2, CR_1.0 and MacaM assemblies, respectively. This suggests that the MacaM assembly is the most complete and accurate of the three available rhesus macaque assemblies. The original NCBI annotation (in GFF format) of the rheMac2 assembly contains 20,973 genes. However, onlyMax contig length 219335 Lenvatinib 205919Mean contig length 15354 6414Contig N50 (kb) 28 13Scaffold N50 (kb) 6760 1707Contig statistics based on contigs placed on chromosomes.Zimin et al. Biology Direct 2014, 9:20 http://www.biologydirect.com/content/9/1/Page 8 ofTable 5 Comparison of rhesus proteins extracted from rheMac2 and MacaM annotation files with human orthologsAnnotation rheMac2_N MacaM Identity 90.93 97.02 Similarity 92.28 98.16 Gaps 41.86 1.rheMac2_N: NCBI annotation of rheMac2. MacaM: Our annotation of the new MacaM assembly. Values equal the mean percent Identities, Similarities and Gaps when comparing rheMac2_N and MacaM with human orthologs.derived from intronic sequence, was substituted for the correct protein sequence encoded by exon 3. A correct protein sequence encoded by exon 3 was derived from MacaM because the scaffold containing exon 3 was correctly assembled which was not the case for rheMac2 [3] or, apparently, CR_1.0 (Figure 2). This demonstrates an important principle: better genome assemblies permit better annotations.mRNA expression studies with MacaM11,265 of these have been assigned informative gene names. The rest have generic names, most commonly a “LOC” prefix followed by a number. The rhesus proteins derived from our annotation of the MacaM assembly are much more similar to their human orthologs than those derived from the NCBI annotations of rheMac2 PubMed ID:https://www.ncbi.nlm.nih.gov/pubmed/16474207 (Table 5, Additional file 4). We were able to annotate genes in MacaM whose exons had been split by misassemblies in rheMac2 [3] but which were contiguous in the MacaM assembly (Figure 2). We used this case (the SHE gene) to assess the annotations for rheMac2 and CR_1.0 (Figure 3). A search for SHE at the RhesusBase database indicated that no gene was found. We were able to identify proteins that appeared to correspond to the SHE protein in MacaM, rheMac2 (both NCBI and Ensembl annotations) and CR_1.0. We aligned these sequences against the human SHE protein sequence. The MacaM sequence was highly similar to the human SHE protein sequence. We found that a portion of the protein sequence encoded by exon 1 was missing in CR_1.0. The protein sequence encoded by exon 3 was missing from the NCBI annotation of rheMac2. For the Ensembl annotation of rheMac2 and CR_1.0, spurious sequence, presumablyWhen we compared mRNA-seq expression in three tissues (testis, thymus and caudate nucleus), we found that substantially more named genes were reported as expressed when the MacaM rhesus genome was used as compared to NCBI annotation of rheMac2 (Table 6). To compare the performance of the rheMac2 and MacaM genomes on a `real-world’ mRNA-seq dataset, we examined the effects PubMed ID:https://www.ncbi.nlm.nih.gov/pubmed/18218841 of an acute stressor on a background of chronic stress in social-housed female rhesus macaques. Social subordination in macaques is a natural stressor that produces distinct stress-related phenotypes and chronically stressed subordinate subjects [40]. We drew blood from both dominant and subordinate animals; following this, we exposed both to an acute stressor (human intruder paradigm [41]) and then drew blood at different time points after exposure. mRNA-seq readmapping was significantly higher with MacaM as compared to rheMac2.