Figure 1. (A) The population identify for the newly sequenced sample
based on PCA analysis. The arrow shows the sample sequenced in this
study. (B) The completeness with Benchmarking Universal Single-Copy
Orthologs (BUSCO) for the final reference genome. (C) The numbers of
unique and sharing SVs for three methods of SVs identification (Vulcan,
NanoSV, and SyRI). (D) The number of long SVs (1Kb) within chromosomes.
The linear regression was based on the autosomes (“lm” function in R
platform, p < 0.001).
Figure 2. The distribution pattern of methylation frequencies across
mitochondrial genome, autosomes, and sex chromosomes based on boxplot
(A) and density plot (B). Only the “minimum (Q1 -1.5*IQR)”, first
quartile [Q1], median, third quartile [Q3] and “maximum (Q3 +
1.5*IQR)” are shown for boxplot.
Figure 3. (A) The methylation frequencies of annotated SNPs within and
around protein-coding genes. The tiny black bars show the standard
errors. (B) Boxplots for methylation frequencies of SNPs with
annotations of impacts on gene structure (following the annotation of
SnpEff v5.1). (C) Boxplots for methylation frequencies of SVs from three
different tools. (D) The median methylation frequencies across small
Indels with different lengths. The formulas show linear regressions of
median values against lengths of small Indels (< 50bp).
Figure 4. The distributions of common logarithm of recombination rates
for SVs. (A) The boxplot comparisons for duplications, inversions,
deletions, and insertions identified from three methods (NanoSV, SyRI,
and Vulcan). The “body”, “down1k”, and “up1k” indicate the regions
within the SVs, 1Kb downstream of the SVs, and 1Kb upstream of the SVs,
respectively. “NS” indicates “non-significant” based on the Wilcoxon
rank sum test (p>0.05). The significance levels of 0.05,
0.01, and 0.001 are showed with “*”, “**”, and “***”,
respectively. (B) The density distribution of the fine-scale
recombination rates for four types of SVs. The “INS”, “INV”,
“DUP”, and “DEL” indicate the “insertions”, “inversions”,
“duplications”, and “deletions”, respectively.
Figure 5. The selective signals for the Chinese and Indian rhesus
macaques based on three complementary methods (Fst,θ π_India/θ π_China,
Ihh12, top 5% strongest windows, 100Kb). (A) The distribution of
Fst andθ π_India/θ π_China based
on comparison between the Chinese and Indian rhesus macaques. The red
and blue points show the the candidate selective sweep windows for the
Indian and Chinese groups, respectively. (B) The candidate selective
sweep signals above the dotted line (top 5% windows) for the Chinese
rhesus macaques. The SVs involved gene (TTC28 ) with the highest
signal in Ihh12 was shown. (C) The candidate selective sweep signals
above the dotted line (top 5% windows) for the Indian rhesus macaques.
The SVs involved gene (IL1RAPL2 ) with the highest signal in Ihh12
was shown. (D) The functional enrichment ontology for the Chinese rhesus
populations. (E) The percentages of SVs under positive selection. (F)
The chromosomal distribution for the 53 positively selected genes with
signals of congruent SVs. Note: the horizontal axis shows the X
chromosome while the vertical axis shows the number of genes. (G) The
linear regression for congruent SVs counts and the SVs under selective
sweep (p = 0.4, not significant). The blue point is the outlier (X
chromosome).
Supplementary figure 1. The whole genome alignment between CR2 and
reference genome of an Indian rhesus macaque (mm10) using minimap2
(-xasm10). The dotplot visualization was based on a R package dotPlotly.
The vertical axis shows the CR2 scaffolds while the horizontal axis
exhibits the chromosomes of mm10.
Supplementary figure 2. The chromosome-wide methylation frequencies for
the Chinese rhesus macaque. The black points show the median values
within slide-windows (the window-size of 1Mb).
Supplementary figure 3. The fine-scale recombination rates inferred with
pyrho package across chromosomes [33], which using population
genomic data of the Chinese and Indian rhesus macaque (27 samples). The
vertical axis is the logarithm of median fine-scale recombination rates
with base 10 (ρ/Mb, slide-window, 1Mb). The horizontal axis shows the
coordinates of chromosomes (Mb).