Fig. 8: Ape SDs and new genes.
a, Comparative analysis of primate SDs comparing the proportion of acrocentric (Acro), interchromosomal (Inter), intrachromosomal (Intra) and shared interchromosomal and intrachromosomal SDs (Shared). The total SD megabases per genome is indicated above each histogram, with the coloured dashed lines showing the average Asian, African great ape and non-ape SD (MFA, Macaca fascicularis78; see Supplementary Fig. XXI.71 for additional non-ape species comparison). b, A violin plot distribution of pairwise SD distance to the closest paralogue for which the median (black line) and mean (dashed line) are compared for different apes (see Supplementary Fig. XXI.72 for all species and haplotype comparisons; n = 17,703, 17,800, 19,979 and 21,066 of SD pairs for chimpanzees, humans and Bornean and Sumatran orangutans, respectively). The box indicates the interquartile range. An excess of interspersed duplications (one-sided Wilcoxon rank sum test; P < 2.2 × 10−16) was observed for chimpanzees and humans when compared to orangutans. c, Alignment view of chromosome 1 double-inversion for gorillas. Positive alignment direction is indicated in grey and negative as yellow. SDs and those with inverted orientations are indicated by blue rectangles and green arrowheads. The locations where the JMJD7–PLA2G4B gene copies were found are indicated by the red arrows. d, Duplication unit containing three genes, including JMJD7–PLA2G4B. e, Multiple sequence alignment of the translated JMJD7–PLA2G4B predicated protein-coding genes. Each sequence is represented by chromosome number and copy number index. Match, mismatch and gaps are indicated with respect to their position in the linear amino acid sequence by blue, red and white, respectively. Regions corresponding to each of JMJD7 or PLA2G4B are indicated by the track below. Data are for haplotype 1. f, Alignment view of chromosome 16q. The expansion of GOLGA6, GOLGA8, HERC2 and MCTP2 genes are presented in the top track. Recurrent inversions between species (yellow) are projected to the human genome with respect to genomic disorder breakpoints (BP1–BP5) at chromosome 15q. The track at the bottom indicates the gene track with GOLGA8 human orthologue in red. InvDup, inverted duplications. g, Multiple sequence alignment of the translated GOLGA8.
