Discussion
One of core tenets in biology is that organisms adapt through natural selection on genomic variants to tackle ever-changing challenges. For evolutionary biologists of rhesus macaque, the genomic variants were of interest for addressing questions involving population demography [24], gene flow [78], disease variants [19], and natural selection [26]. At species level, rhesus macaque was reported to cover 2.5 times higher overall nucleotide diversity than humans, empowering this species as a great reservoir to discover and model corresponding pathogenic variants in human [19, 24]. At population level, the Chinese subspecies was found to host higher genomic diversity and higher effective population size (Ne ) than the Indian subspecies [24, 26]. Thus, macaque species could serve as a powerful model to study intra-specific variants.
In medical and population genetics, structural variations (SVs, >50bp) are known with more pronounced phenotypic impacts than SNPs [79, 80]. Thus, SVs have increasingly become characterized in studies of human diseases including mental disorders and cancers [81]. However, as a critical medical model for human disease, the rhesus macaque was rarely investigated in issues related to the SVs. In this study, we initially presented a chromosome-level reference genome for a Chinese rhesus macaque (CR2) with both Nanopore long and Illumina short reads. Based on this reference and the nanopore long reads, we identified SVs between the Chinese and Indian subspecies and investigated their patterns and their relationship with methylation frequencies, recombination rates, and evolutionary forces.
We found that X chromosome is an obvious outlier for the significant linear pattern that shapes the number of SVs across autosomes. In addition, we detected significantly higher contribution of X-chromosomal SVs-involved genes to the reservoir of genes under selective sweep. These patterns are consistent with the well-known “faster-X effect”, which predicts that the X chromosome has a higher rate of adaptive evolution than the autosomes [63, 82, 83]. Although the “faster-X effect” is a generalization for the evolutionary divergence at the species level, our result suggests that the effect is more taxonomically pervasive than previously thought, especially at the subspecies level. Moreover, for medical genetics, the recognition of the “faster-X effect” at the population level could be informative to the dominance/recessivity of deleterious mutations leading to genetic diseases [28, 63, 84].
Taking advantages of nanopore data in providing information of DNA cytosine methylation [65], we estimated the methylation frequencies of the CR2 at a genome-wide scale. Previously, controversial conclusions were made for the methylation levels of mitochondrial genome relative to nuclear genome [85]. Very low or no methylation for mitochondrial genome was found by some studies [86, 87], although some contradictory conclusions were also made [88, 89]. Based on nanopore long reads, we found that mitochondrial genome has over 25 times lower median methylation frequency than nuclear chromosomes, thus providing evidence for the very low methylation level of mitochondrial genome. Interestingly, we found significantly lower methylation level for duplications than for other types of SVs (deletions, insertions, and inversions). Previous studies have found that the regions with decreased methylation tend to have higher GC content [90] and duplications demonstrate significantly higher GC content than non-duplications [91]. Thus, our finding of the decreased methylation level in duplications based on nanopore long reads is consistent with the implications of previous findings.
Duplications and other types of SVs are derived from the intergenerational mixing of DNA through homologous recombination during meiosis [92]. However, the relationship between recombination rates and different types of SVs is less clear. The yeast model has revealed that duplication is associated with the increased recombination rates [93]. In this study, we revealed significantly higher recombination rates in duplications than in other types of SVs. Half a century ago, Susumu Ohno has already proposed the notion of duplication as the major source of adaptive innovation during the long-term evolution [94]. Thus, the higher recombination rates may facilitate the evolution of duplications by boosting the efficiencies of purifying selection to remove deleterious duplications on the one hand, and positive selection to increase beneficial duplications on the other [95].
Consistent with the expectation of SVs as important raw materials upon which natural selection can then play, we found that over 3% of SVs may be under selective sweep. Moreover, over 3% of positively selected genes host signals of SVs. Some of these SVs-involved genes under positive selection have been reported with genetic defects related to human diseases. For example, the SCN1A , coding for the α-subunit of the neuronal voltage-gated sodium ion channel, type 1 (NaV 1.1), is correlated with human epileptic encephalopathies [96]. The genesIL1RAPL2 , ACSL4 , and PAK3 are related to disease phenotypes including Alport syndrome, elliptocytosis, and intellectual disability [97, 98]. Interestingly, SLC25A19 , a mitochondrial deoxyribonucleotide transporter, is related to severe congenital microcephaly (reduced brain size) [99-101]. From the perspectives of evolutionary biology and translational medicine, the SVs-involved genetic changes and the related positive selection in rhesus macaques could not only provide useful insights into the species- or subspecies-specific adaptation, but also facilitate the translational studies from nonhuman primate models to human. Altogether, our study and historical research may embark a promising journal to explore SVs-derived adaptive evolution and functional effects from the nonhuman primate models to our own species.