(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%.
Matchmaking between recombination and you can GC-blogs
Because of the observation, i estimate you to typically a 1 cm/Mb rise in recombination price was of the a rise in GC articles of around 0.5%. Alternatively a-1% upsurge in GC posts represents http://datingranking.net/gleeden-review/ an approximately 2 cM/Mb rise in recombination speed. I finish you to definitely because of the obvious rarity away from NCO gene transformation, at the very least on the bee genome, extrapolation regarding GC articles to mediocre crossing-more rate thus seems to be justifiable, no less than to have GC blogs more than 20%. We notice too you to at the significant GC material new recombination rate tends to be over or underestimated. This might mirror an effective discordance ranging from current and you will prior recombination cost.
Talking about familiar with create Profile 4B, and that gift ideas a relatively sounds-totally free (immediately following smoothing) monotonic dating between them parameters
Crossing-more than speed is additionally of nucleotide diversity, gene occurrence, and duplicate amount version regions (Profile S11-S13 into the More file step 1) . Provided the removal of hetSNPs off research the latter result is maybe not trivially an effective CNV relevant artifact. All of our good-level analyses let you know a positive relationship ranging from nucleotide variety and you may recombination speed anyway the latest scales away from 10, one hundred, 200, or five-hundred kb succession screen (Figure S11 from inside the Even more document step one). This bolsters past analyses, one of and this advertised the new pattern however, found it become non-tall, while several other reported a pattern between people genetic estimates regarding recombination and you may hereditary diversity. Brand new pattern accords toward perception one recombination causes shorter Slope-Robertson interference therefore permitting significantly lower rates from hitchhiking and you can history options, thus helping better assortment. I plus select an effective negative relationship ranging from recombination and you can gene thickness (Profile S12 within the More document step one) and you can a robust self-confident relationship ranging from recombination while the period of multi-content places in the various window brands (Profile S13 inside A lot more document 1). Brand new correlation that have CNVs is actually in line with a role to possess non-allelic recombination generating duplications and deletions via irregular crossing over .
