The analysis of the distribution of ? along chromosomes at the 100-kb scale reveals a more uniform distribution than that of CO (c) rates, with no reduction near telomeres or centromeres (Figure 5). More than 80% of 100-kb windows show ? within a 2-fold range, a percentage that contrasts with the distribution of CO where only 26.3% of 100-kb windows along chromosomes show c within a 2-fold range of the chromosome average. To test specifically whether the distribution of CO events is more variable across the genome that either GC or the combination of GC and CO events (i.e., number of DSBs), we estimated the coefficient of variation (CV) along chromosomes for each of the three parameters for different window sizes and chromosome arms. In all cases (window size and chromosome arm), the CV for CO is much greater (more than 2-fold) than that for either GC or DSBs (CO+GC), while the CV for DSBs is only marginally greater than that for GC: for 100-kb windows, the average CV per chromosome arm for CO, GC and DSBs is 0.90, 0.37 and 0.38, respectively. Nevertheless, we can also rule out the possibility that the distribution of GC events or DSBs are completely random, with significant heterogeneity along each chromosome (P<0.0001 at all physical scales analyzed, from 100 kb to 10 Mb; see Materials and Methods for details). Not surprisingly due to the excess of GC over CO events, GC is a much better predictor of the total number of DSBs or total recombination events across the genome than CO rates, with semi-partial correlations of 0.96 for GC and 0.38 for CO to explain the overall variance in DSBs (not taking into account the fourth chromosome).

DSB solution involves the development out of heteroduplex sequences (for CO or GC situations; Shape S1). These types of heteroduplex sequences normally have A beneficial(T):C(G) mismatches which can be repaired randomly otherwise favoring specific nucleotides. During the Drosophila, there’s absolutely no direct experimental research supporting Grams+C biased gene conversion process fix and you will evolutionary analyses enjoys provided contradictory overall performance while using CO rates as an excellent proxy having heteroduplex creation (– but pick , ). Note yet not you to definitely GC situations be a little more constant than simply CO occurrences within the Drosophila plus in most other organisms , , , which GC (?) rates will be way more associated than CO (c) prices whenever investigating the brand new possible outcomes regarding heteroduplex repair.

In a few species, gene sales mismatch fix has been proposed is biased, favoring Grams and you may C nucleotides – and you will anticipating a positive matchmaking anywhere between recombination pricing (sensu Sikh dating review volume out of heteroduplex creation) and the Grams+C posts of noncoding DNA ,

Our very own research show no connection out of ? which have G+C nucleotide constitution at intergenic sequences (Roentgen = +0.036, P>0.20) otherwise introns (R = ?0.041, P>0.16). The same not enough association is observed when Grams+C nucleotide constitution is compared to the c (P>0.twenty-five for both intergenic sequences and introns). We find for this reason no proof of gene conversion bias favoring G and you may C nucleotides into the D. melanogaster according to nucleotide structure. The reasons for the majority of one’s past abilities one inferred gene conversion prejudice towards Grams and C nucleotides inside Drosophila may be multiple you need to include employing simple CO maps also because the incomplete genome annotation. Due to the fact gene density in D. melanogaster is actually highest when you look at the nations having low-reduced CO , , the countless has just annotated transcribed places and G+C steeped exons , , was prior to now examined due to the fact basic sequences, particularly in this type of genomic countries which have non-less CO.

The fresh new design from recombination in the Drosophila

To discover DNA motifs associated with recombination events (CO or GC), we focused on 1,909 CO and 3,701 GC events delimited by five-hundred bp or less (CO₅₀₀ and GC₅₀₀, respectively). Our D. melanogaster data reveal many motifs significantly enriched in sequences surrounding recombination events (18 and 10 motifs for CO and GC, respectively) (Figure 6 and Figure 7). Individually, the motifs surrounding CO events (M_CO) are present in 6.8 to 43.2% of CO₅₀₀ sequences, while motifs surrounding GC events (M_GC) are present in 7.8 to 27.6% of GC₅₀₀ sequences. Note that 97.7% of all CO₅₀₀ sequences contain at least one M_CO motif and 85.0% of GC₅₀₀ sequences contain one or more M_GC motif (Figure S4).

saarcis

See all author post