Comparative Genomic Analysis Identifies Great-Ape-Specific Structural Variants and Their Evolutionary Relevance

Abstract

During the origin of great apes about 14 million years ago, a series of phenotypic innovations emerged, such as the increased body size, the enlarged brain volume, the improved cognitive skill, and the diversified diet. Yet, the genomic basis of these evolutionary changes remains unclear. Utilizing the high-quality genome assemblies of great apes (including human), gibbon, and macaque, we conducted comparative genome analyses and identified 15,885 great ape-specific structural variants (GSSVs), including eight coding GSSVs resulting in the creation of novel proteins (e.g., ACAN and CMYA5). Functional annotations of the GSSV-related genes revealed the enrichment of genes involved in development and morphogenesis, especially neurogenesis and neural network formation, suggesting the potential role of GSSVs in shaping the great ape-shared traits. Further dissection of the brain-related GSSVs shows great ape-specific changes of enhancer activities and gene expression in the brain, involving a group of GSSV-regulated genes (such as NOL3) that potentially contribute to the altered brain development and function in great apes. The presented data highlight the evolutionary role of structural variants in the phenotypic innovations during the origin of the great ape lineage.

Keywords: body size; brain; comparative genomics; great apes; structural variant.

Fig. 1.

Identification and annotation of GSSVs. (A) The cladogram indicates the phylogenetic relationship among the analyzed primate species. We used the high-quality genomes of four great ape species, one lesser ape species, and one Cercopithecidae species. The numbers of SVs and their genomic lengths based on assembly comparisons are indicated. DELs are the numbers above the lines and INSs are those beneath the lines. The number in the box indicates the identified 15,885 GSSVs, including 7,728 DELs and 8,157 INSs. (B) Chromosomal distribution of the identified GSSVs. The number of SVs is tightly correlated with the length of the chromosome, as indicated by the Pearson correlation (R² = 0.95, P = 6.7e⁻¹³). (C) The size distribution of GSSVs. The two peaks at 300 bp and 6 kb indicate the Alu and L1 elements, respectively. (D) Annotation of GSSVs located in the repeat regions of the genome, where SINEs (such as Alu) and LINEs (such as L1) compose of the great majority of the identified GSSVs.

Fig. 2.

Functional annotations of the identified HC-GSSVs. (A) The ratios of the high-confident and the complex GSSVs after manual curation. (B) The pie plot shows the functional annotations of HC-GSSVs using the VEP tool. (C, D) The results of GO enrichment analysis of the 2,353 HC-GSSV-related genes. (E) A 60-bp deletion located in exon-12 of ACAN, a gene related to skeletal development. (F) A 264-bp insertion located in exon-2 of CMYA5, a well-known gene related to schizophrenia. The local sequence alignments (DNA and protein sequences) among mammalian species together with the MUMmer plots showing the locations of the GSSVs are presented.

Fig. 3.

The HC-GSSVs located in the CREs of the brain. (A) The HC-GSSV-related genes showing human–chimp-specific CRE activity (by the H3K27ac signals) and gene expression changes (by RNA-seq) compared with macaque across seven brain regions, including CB, CN, OP, PcGm, PFC, Put, and TN. (B) Ranking of the 43 upregulated genes based on gene expression and the H3K27ac signals.

Fig. 4.

Overview of GSSV occurred in NOL3. (A) A 297-bp INS located in a human-chimpanzee-specific CRE (blue region) in which the nearest human–chimpanzee-specific gene is NOL3. The left plot shows the difference of H3K27ac signal in OP region among human, chimpanzee, and rhesus monkey; the right plot shows the MUMmer plot of the 297-bp INS between great apes and gibbon; and bottom plot shows multiple sequence alignments of representative primate species. (B) The comparisons of normalized read count of H3K27ac signal of CRE (left) and expression (right) of NOL3. NS, not significant; *P < 0.05; **P < 0.01. (C) TF enrichment of CREs. The CREs with human-chimpanzee-specific TF binding sites are denoted in red scatters, and two ZNF460 binding sites are labeled, which have the highest FIMO score and located in SV region (gray region). (D) Summary of brain-related genes with human–chimp-specific CREs and overlapped to identified GSSVs.