(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%.
Relationship anywhere between recombination and you can GC-posts
Because of the observance, i imagine getiton one to typically a-1 cm/Mb upsurge in recombination rate was with the a boost in GC stuff around 0.5%. However a-1% escalation in GC stuff represents a roughly dos cM/Mb boost in recombination rate. I ending one because of the noticeable rarity out of NCO gene conversion process, about about bee genome, extrapolation out-of GC articles so you’re able to average crossing-more than price for this reason is apparently justifiable, no less than getting GC articles more 20%. I mention also one during the tall GC information the fresh recombination price is more or underestimated. This might echo an effective discordance anywhere between most recent and you may earlier recombination costs.
These are always make Shape 4B, which gift suggestions a relatively music-free (shortly after smoothing) monotonic matchmaking among them details
Crossing-over speed is additionally in the nucleotide assortment, gene occurrence, and you may copy matter adaptation nations (Profile S11-S13 for the Extra file 1) . Offered all of our elimination of hetSNPs regarding research aforementioned result is maybe not trivially an excellent CNV associated artifact. All of our good-measure analyses tell you a confident relationship anywhere between nucleotide range and recombination price at all the newest bills off 10, one hundred, 200, or five-hundred kb series windows (Profile S11 when you look at the Extra document step 1). That it bolsters early in the day analyses, certainly which stated new pattern however, found it to be non-extreme, while other stated a trend ranging from populace hereditary rates from recombination and you can genetic variety. The pattern accords to the sense one to recombination grounds smaller Slope-Robertson disturbance therefore providing significantly lower rates off hitchhiking and you may record selection, therefore providing greater variety. We along with look for a robust bad relationship ranging from recombination and gene thickness (Contour S12 during the More document step one) and you can a robust positive relationship anywhere between recombination additionally the length of multi-backup nations in the individuals windows products (Shape S13 in the Extra file 1). The new relationship having CNVs try in keeping with a role having low-allelic recombination promoting duplications and you will deletions via unequal crossing-over .