the same consequently they are breakpoints associated with the high GC posts just like the questioned if CO breakpoints try where CO-relevant gene conversion process is actually acting?

As regards the next topic, we in fact discover that the latest breakpoint regions have large GC content than the surrounding regions hence this new directly surrounding re also-gions possess large GC-articles compared to the genome average and/or at random simulated data (Contour 4A and you will Profile S10 when you look at the A lot more file 1).

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). Re-moving these three results in a more consistent trend

This also suggests that less than circa 20% GC the newest recombination speed are no (Extra file step one: Contour S10F)

(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%.

Speaking of regularly create Profile 4B, hence presents a relatively appears-free (shortly after smoothing) mono-tonic relationships between the two variables

Of the observation, i estimate you to definitely on average a-1 cm/ Mb boost in recombination rate is on the a boost in GC content of around 0.5%. Con-versely a 1% increase in GC articles represents an approximately dos cM/Mb boost in recombination rates. We ending you to definitely because of the visible rareness from NCO gene conversion process, at least regarding bee genome, extrapola-tion out of GC stuff to average crossing-more than price thus appears to be justifiable, at the very least to own GC stuff more 20%. We mention also one to on high GC material the brand new re-integration speed is generally more than otherwise underestimated. This might mirror a beneficial discordance ranging from latest and you may earlier in the day re also-combination cost.

Crossing-more than price is also regarding the nucleotide diversity, gene occurrence, and you may copy number type re-gions (Figure S11-S13 in the Extra document step 1) . Offered our very own removal of hetSNPs away from research aforementioned result is maybe not trivially a CNV relevant artifact. The great-measure analyses inform you a confident relationship anywhere between nucleotide diversity and recombination rates after all the fresh scales off 10, a hundred, two hundred, otherwise five hundred kb sequence windows (Profile S11 within the More document 1). That it bolsters previous analyses, certainly one of and therefore stated the fresh new trend but found it datingranking.net local hookup Sioux Falls SD to-be non-tall, if you’re several other claimed a pattern ranging from inhabitants hereditary estimates away from recombination and you can gen-etic variety. The latest trend accords into belief that lso are-consolidation reasons quicker Hill-Robertson disturbance ergo permitting significantly lower rates off hitchhiking and you will back-crushed choices, therefore enabling greater diversity. I and additionally find a powerful negative relationship between recombin-ation and you may gene thickness (Contour S12 in Even more file 1) and you can an effective confident correlation anywhere between recombination as well as the period of multi-duplicate nations at individuals screen versions (Contour S13 within the More document step 1). The fresh new relationship which have CNVs try in keeping with a task for non-allelic re also-integration creating duplications and deletions thru uneven crossing over .