(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%.
Relationships anywhere between recombination and you can GC-articles
By the observation, we guess you to definitely an average of a 1 cm/Mb increase in recombination speed are of this a boost in GC stuff of about 0.5%. However a 1% rise in GC articles corresponds to a more or less dos cM/Mb escalation in recombination rates. I finish one considering the noticeable rarity away from NCO gene transformation, at least about bee genome, extrapolation off GC content so you’re able to average crossing-more than speed therefore seems to be justifiable, at the very least to own GC posts more 20%. I mention also one at significant GC articles the recombination rates can be more than otherwise underestimated.