(A) GC content variance around CO breakpoints (blue dots and line). The window 0 on the x-axis is the GC content of the breakpoints and the negative and positive values represent the distance away from the breakpoints. Each of these windows is defined as 2 kb sequence and the GC content is calculated for each window. The red dots and line are one of the GC content random samples simulated like the numbers of CO breakpoints (blue dot and line). After 10,000 repeats, not one of random samples is as extreme as the observed (blue line) (P <0.0001). (B) Relationship between recombination and GC content. When the chromosomes are dissected into 10 kb non-overlapping regions, recombination rate (cM/Mb) and GC content can be obtained for each of them. After the bins are sorted by the GC content, the windows are divided into 31 groups based on GC content (approximately 20% to 51%, 1% interval), and the average (and s.e.m.) recombination rates reported for each group.
In both we dissect the genome into 10 kb non-overlapping windows of which there are 19,297. First, we ask about the raw correlation between GC% and cM/Mb for these windows, which as expected is positive and significant (Spearman’s rho = 0.192; P <10 -15 ). Second, we wish to know the average effect of increasing one unit in either parameter on the other. Given the noise in the data (and given that current recombination rate need not imply the ancestral recombination rate) we approach this issue using a smoothing approach. We start by rank ordering all windows by GC content and then dividing them into blocks of 1% GC range, after excluding windows with more than 10% ‘N'. The resulting plot is highly skewed by bins with very high GC (55% to 58%) as these have very few data points (Additional file 1: Figure S10E) (the same outliers likely effect the raw correlation too). Removing these three results in a more consistent trend (Additional file 1: Figure S10F). This also suggests that below circa 20% GC the recombination rate is zero (Additional file 1: Figure S10F). Removing those with GC <20% and, more generally, any bins with fewer than 100 windows (all bins with GC < 20% have fewer than 100 windows) leaves 18,680 (96.8%) of the windows, these having a GC content between approximately 20% and 51%.
Dating between recombination and you may GC-blogs
Of the observance, i estimate you to definitely an average of a-1 cm/Mb boost in recombination rate is actually with the a rise in GC posts of around 0.5%. In contrast a 1% rise in GC posts represents a roughly dos cM/Mb boost in recombination speed. I stop one to considering the visible rareness out-of NCO gene conversion, no less than on bee genome, extrapolation out-of GC blogs to mediocre crossing-more rates hence appears to be justifiable, at the least for GC stuff more than 20%. We mention too one from the tall GC content material the new recombination speed is over or underestimated. This might reflect an effective discordance anywhere between newest and you may previous recombination prices.
Talking about always construct Shape 4B, which gift suggestions a comparatively looks-totally free (immediately after smoothing) monotonic matchmaking among them details
Crossing-more than speed is also from the nucleotide variety, gene thickness, and you will content number type nations (Figure S11-S13 within the Additional document step one) . Given our very own elimination of hetSNPs out of studies the latter outcome is maybe not trivially a good CNV associated artifact. All of our good-size analyses reveal a confident relationship ranging from nucleotide diversity and you may recombination rate at all the fresh balances connexion discount code out of 10, one hundred, two hundred, otherwise five-hundred kb sequence window (Figure S11 during the More file step 1). That it bolsters previous analyses, one of and that reported the pattern but found it as non-significant, when you find yourself some other said a pattern anywhere between inhabitants hereditary estimates off recombination and you may hereditary variety. New trend accords to the opinion one to recombination reasons shorter Mountain-Robertson interference therefore permitting significantly lower rates off hitchhiking and record choices, therefore providing higher assortment. We plus see a robust negative relationship anywhere between recombination and gene occurrence (Figure S12 in Extra document 1) and you will a robust self-confident correlation anywhere between recombination additionally the length of multi-duplicate nations in the certain screen systems (Shape S13 within the A lot more file 1). The fresh relationship with CNVs is in keeping with a role to have low-allelic recombination creating duplications and you can deletions thru unequal crossing-over .