(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 ranging from recombination and you may GC-posts

By the observation, i estimate that on average a-1 cm/Mb upsurge in recombination price try associated with a boost in GC posts of around 0 cougar life.5%. Alternatively a-1% increase in GC blogs represents an approximately 2 cM/Mb increase in recombination speed. I stop you to considering the obvious rarity away from NCO gene sales, at the very least regarding bee genome, extrapolation regarding GC articles so you can mediocre crossing-over speed thus seems to be justifiable, about to own GC stuff more than 20%. I note as well one to during the extreme GC contents the fresh recombination price can be more or underestimated. This may mirror a beneficial discordance anywhere between most recent and you will prior recombination cost.

These are accustomed build Figure 4B, which presents a fairly looks-free (immediately following smoothing) monotonic dating among them details

Crossing-over rate is additionally in the nucleotide assortment, gene occurrence, and you will copy number version regions (Profile S11-S13 into the A lot more file step 1) . Given our very own removal of hetSNPs from analysis aforementioned result is maybe not trivially an excellent CNV related artifact. The great-scale analyses let you know an optimistic relationship between nucleotide variety and recombination price anyway the newest bills of 10, one hundred, two hundred, or 500 kb succession screen (Contour S11 in Even more document step 1). Which bolsters previous analyses, certainly one of which claimed the brand new pattern but think it is become non-high, if you are other advertised a trend anywhere between inhabitants hereditary quotes out of recombination and you can hereditary variety. The newest pattern accords on belief you to definitely recombination grounds reduced Slope-Robertson interference therefore providing reduced rates from hitchhiking and you can record solutions, very providing deeper assortment. I and find a robust negative correlation anywhere between recombination and you can gene density (Figure S12 from inside the Most document 1) and you can a robust confident relationship between recombination and the length of multi-copy places within individuals screen items (Profile S13 in the More file step one). The brand new correlation having CNVs is in line with a task to own non-allelic recombination producing duplications and you will deletions through unequal crossing over .