Lack of biased gene conversion process repair favoring G/C nucleotides inside D. melanogaster

Lack of biased gene conversion process repair favoring G/C nucleotides inside D. melanogaster

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 resolution requires the development regarding heteroduplex sequences (for both CO or GC situations; Profile S1). This type of heteroduplex sequences is also consist of Good(T):C(G) mismatches which can be fixed randomly or favoring certain nucleotides. When you look at the Drosophila, there is absolutely no lead fresh evidence help G+C biased gene transformation repair and you may evolutionary analyses possess provided inconsistent overall performance when using CO prices because the a great proxy having heteroduplex development (– however, look for , ). Note yet not you to GC events are more regular than CO occurrences inside Drosophila along with almost every other organisms , , , and therefore GC (?) pricing should be significantly more related than CO (c) costs when examining the fresh new possible outcomes regarding heteroduplex resolve.

In some types, gene transformation mismatch repair could have been recommended are biased, favoring G and you may C nucleotides – and forecasting an optimistic relationship ranging from recombination cost (sensu regularity away from heteroduplex formation) additionally the Grams+C blogs from noncoding DNA ,

Our investigation tell you zero organization regarding ? which have Grams+C nucleotide constitution in the intergenic sequences (Roentgen = +0.036, P>0.20) otherwise introns (R = ?0.041, P>0.16). The same decreased relationship sometimes appears when G+C nucleotide constitution is actually compared to c (P>0.25 for intergenic sequences and you will introns). We find ergo no proof of gene sales prejudice favoring Grams and you can C nucleotides from inside the D. melanogaster according to nucleotide composition. The reasons for many of earlier in the day show you to inferred gene conversion prejudice towards Grams and you will C nucleotides within the Drosophila is generally several you need to include the utilization of simple CO charts as well just like the partial genome annotation. Because gene thickness when you look at the D. melanogaster is higher during the places having non-quicker CO , , the numerous has just annotated transcribed regions and you may Grams+C steeped exons , , might have been prior to now analyzed as the neutral sequences, especially in these types of genomic nations with low-quicker CO.

The newest design away from recombination from inside 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 Russian dating apps events (18 and 10 motifs for CO and GC, respectively) (Figure 6 and Figure 7). Individually, the motifs surrounding CO events (MCO) are present in 6.8 to 43.2% of CO500 sequences, while motifs surrounding GC events (MGC) are present in 7.8 to 27.6% of GC500 sequences. Note that 97.7% of all CO500 sequences contain at least one MCO motif and 85.0% of GC500 sequences contain one or more MGC motif (Figure S4).

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