Figure 2:

Schematic diagrams illustrating assembly and annotation errors in the rhesus macaque draft genome. (A) Scaffold assigned to the wrong chromosome: The scaffold containing exons 1, 2, 4, 5, and 6 of the SRC homology 2 domain containing E (SHE) gene is correctly assigned to chromosome 1 in the rhesus draft genome. However, the scaffold containing exon 3 of the SHE gene was incorrectly assigned to chromosome X. (B) Scaffold with exon in the wrong orientation: An unlocalized scaffold from the draft rhesus genome contains exons 9-13 of the Bardet-Biedl syndrome 1 (BBS1) gene. It was not included in the rhesus chromosome 14 file with the scaffold that contains exons 1-8 of BBS1. This is likely the contig containing exon 9 was in the wrong orientation with respect to the rest of the scaffold. (C) Sequencing error results in apparent nonsense mutation: The rhesus draft genomic DNA had sequencing error in the adrenergic, beta-1, receptor (ADBR1) gene. This introduced a premature stop codon (arrow, top panel). This has resulted in this locus being labeled a pseudogene by NCBI. Our targeted sequencing of this region has revealed the correct sequence (JN589014.1 - bottom panel). (D) Missing exon results in substitution of intronic sequence: The original rhesus draft genome did not contain the sequence for exon 15 for the adenylate cyclase 3 (ADCY3) gene. Instead, intronic sequence between exons 14 and exon 16 was substituted (top panel) when this gene was annotated. This led to spurious protein sequence (original protein) and a premature stop codon. The missing exon 15 was sequenced and deposited in GenBank (HM067826.1). NCBI then corrected the rhesus ADCY3 gene model and now reports a correct protein sequence for this gene (bottom panel). Figure 2 is redrawn from Zhang et al. 2012.