(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 https://datingranking.net/ilove-review/ ranging from recombination and you can GC-content
By the observance, i estimate that on average a 1 cm/Mb rise in recombination price was associated with a rise in GC content of approximately 0.5%. However a 1% escalation in GC stuff corresponds to a more or less 2 cM/Mb rise in recombination speed. I stop one to given the obvious rareness out-of NCO gene transformation, about on the bee genome, extrapolation regarding GC posts so you’re able to average crossing-more speed hence seems to be justifiable, no less than to have GC posts over 20%. We note also you to during the high GC information the fresh new recombination rate are more otherwise underestimated. This might mirror a great discordance ranging from current and you may past recombination costs.
Talking about familiar with create Profile 4B, which merchandise a fairly audio-free (shortly after smoothing) monotonic relationship between them details
Crossing-over speed is also from the nucleotide variety, gene density, and content matter type nations (Profile S11-S13 when you look at the A lot more document step one) . Provided our elimination of hetSNPs of studies aforementioned result is perhaps not trivially an excellent CNV relevant artifact. Our very own fine-size analyses let you know an optimistic correlation between nucleotide diversity and recombination rate anyway the brand new bills off 10, 100, 2 hundred, otherwise 500 kb succession screen (Shape S11 from inside the Additional document step one). Which bolsters early in the day analyses, one of which advertised brand new pattern but found it are non-significant, when you’re another advertised a development ranging from populace hereditary prices out of recombination and you may genetic assortment. The newest development accords into the opinion you to definitely recombination factors faster Hill-Robertson interference therefore helping significantly lower rates regarding hitchhiking and you can record choices, thus helping better range. We and get a hold of a strong bad correlation between recombination and you may gene occurrence (Profile S12 into the Even more file step 1) and you may an effective confident correlation anywhere between recombination and period of multi-duplicate regions at the various windows items (Figure S13 from inside the Even more document step 1). Brand new relationship having CNVs is consistent with a role having low-allelic recombination generating duplications and you can deletions through unequal crossing-over .
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