(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 between recombination and you may GC-blogs
Of the observance, we guess one to on average a-1 cm/Mb rise in recombination rates was associated with a rise in GC posts of around 0.5%. Having said that a 1% escalation in GC content represents an approximately 2 cM/Mb rise in recombination price. I finish one given the apparent rarity from NCO gene conversion process, at the least on bee genome, extrapolation out-of GC articles so you can mediocre crossing-more than speed hence is apparently justifiable, at the least to possess GC stuff more 20%. We note also one to at significant GC content material the recombination price tends to be more than or underestimated. This could echo an effective discordance anywhere between current and earlier recombination prices.
Speaking of regularly construct Figure 4B, and therefore merchandise a relatively looks-totally free (immediately after smoothing) monotonic relationships between the two details
Crossing-over speed is also from the nucleotide variety, gene occurrence, and duplicate matter type nations (Figure S11-S13 into the Most file step 1) . Given our very own removal of hetSNPs of studies aforementioned outcome is maybe not trivially an effective CNV relevant artifact. Our very own good-size analyses let you know an optimistic correlation between nucleotide variety and you will recombination price at all the fresh bills from ten, a hundred, 2 hundred, or five hundred kb series windows (Figure S11 when you look at the Extra file step one). It bolsters prior analyses, one of which claimed this new development but think it is getting non-extreme, if you are other stated a trend between populace countrymatch promo code genetic prices regarding recombination and you will genetic diversity. Brand new trend accords toward insight that recombination explanations smaller Slope-Robertson disturbance hence helping reduced rates from hitchhiking and you will history alternatives, therefore permitting deeper variety. We and additionally pick a strong negative relationship between recombination and you can gene thickness (Figure S12 for the Additional file step 1) and you can a powerful positive relationship anywhere between recombination additionally the period of multi-content regions at the certain screen systems (Shape S13 during the Most file step one). The fresh new relationship which have CNVs is in line with a role for non-allelic recombination producing duplications and you can deletions thru uneven crossing-over .