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.