Genomic correlates away from recombination
Pearson’s correlations along windows of 100 kb were calculated between recombination rates and the following genomic features: nucleotide diversity (?w), gene density (measured as the proportion of base pairs of the window falling into coding regions), GC content (%) and distance from the centromere to the tip of each chromosome arm (in kb). As no information exists regarding the exact position of centromeres in the Eucalyptus chromosomes, and no relationship has been yet established between the pseudochromosomes and the chromosomes in cytological observations, all chromosomes were assumed to be metacentric. Correlation significance was assessed by comparing the calculated values with those of 5000 permuted data sets that maintained the chromosomal order of all observations but that shuffled the relative positions of the two variables (Nordborg et al., 2005 ) using the function ‘sample’ in R.
Abilities
The 2 linkage maps constructed with separate sets of SNPs consisted of 4396 SNPs to own Age. grandis and you may 3991 to have Elizabeth. urophylla, coating comparable complete recombination distances (Fig. 1; Desk S1; Notes S1). All in all, 192 (dos.3%) nonsyntenic SNPs, were omitted, which is SNPs one mapped so you’re able to linkage groups distinctive from the brand new requested ones considering the genome reputation. This new positioning of the Elizabeth. grandis charts to the current genome version 1.step 1 shown system inconsistencies for the multiple chromosomes, even more significantly toward chromosomes step 1, 2, cuatro and you can 8 (Figs step one, dos, S1). Map-mainly based quotes out of recombination cost was in fact comparable towards the several varieties, step 3.18 ± step 1.1 and step three.55 ± 0.8 cM Mb ?step 1 (Dining table S1). This new Yards arey maps (Figs dos, S1) shown a fairly comparable slope out-of recombination price across the chromosomes, and just more compact plateaus from recombination was basically viewed, particularly, toward chromosomes cuatro, 9 and you will ten.
The amount regarding genome-broad linkage disequilibrium from inside the Elizabeth. grandis
Pairwise estimates of r 2 were obtained from haplotype probabilities for all pairwise distances among the Infinium SNPs on each chromosome. A total of 21 351 SNPs, an average of 1941 SNPs per chromosome, with pairwise distances varying from 135 bp up to several Mb, were used in the calculations, resulting in nearly two million pairwise estimates of r 2 per chromosome and over 21 million at the genome-wide scale for 72 sampled genomes of E. grandis. Owing to the very large number of estimates of r 2 and because the LD decay curves become an asymptote thereafter, LD decay plots are shown only up to 50 kb distances. Average genome-wide LD was r 2 = 0.131, decaying to < 0.2 within c. 5.7 kb (half-decay within 4.3 kb) while = 0.123, showing a slightly faster decay within c. 4.9 kb (half-decay within 3.7 kb) (Fig. 3). The small difference between raw and corrected r 2 is consistent with the lack of population structure between the two E. grandis provenances as indicated by the low Fst = 0.041 ± 0.06 previously calculated based on 28 658 genome-wide SNPs (Silva-ong the c. 4000 linkage mapped markers in E. grandis and r 2 plotted against the distance in cM. With map resolution of c. 0.3 cM, corresponding to c. 106 kb, no r 2 estimate was larger than 0.2, consistent with the decay observed at c. 4–6 kb (Fig. S2). No impact of the few assembly inconsistencies of the E. grandis genome version 1.1 was seen on the pattern of LD decay and no difference was observed when rarer SNPs with MAF > 0.01 were included in the estimation of r 2 (Fig. S3).
Population-scaled recombination speed within the Elizabeth. grandis
About three ways to get genome-wide estimates away from ? was indeed undertaken playing with one or two independent fresh research establishes nearby nearly 13 mil SNPs regarding pooled sequence investigation as well as over 21 https://datingranking.net/local-hookup/omaha 100000 Infinium SNPs. Chromosome-particular quotes off ? was in fact acquired a variety of genomic windows items regarding SNP amounts that have LDH from the and H otspotter (Table 1). Prices were determined round the all chromosomes for the 2402 overlapping containers off 15 SNPs (imply bin proportions, 250 kb; SNP thickness, 1/sixteen.7 kb) plus 242 overlapping containers of 105 SNPs (imply container proportions, 2500 kb; SNP occurrence, 1/ kb). Little version is actually viewed between them rates and all over chromosomes. Prices acquired because of the H otspotter was basically in general twice as high as those people away from LDH during the , most likely reflecting the different assumptions concerning your LD make of the brand new a few estimate methods. For that reason, the fresh genome-broad prices out-of productive people types gotten from the equating ? to new recombination rates c was basically plus two times as highest with H otspotter . The new genome-broad rates away from ? gotten which have Infinium SNPs converged to actually similar philosophy and you may magnitudes into the imagine received to your pooled sequencing studies playing with mlRho and also to quotes derived from population-top LD (Table 2). Though some amount of testing bias inherent toward approach appears to get present when you compare the latest estimates out-of ? from H otspotter and you will mlRho and have within rates of LDH on and you may society-top LD, the values didn’t disagree by the > 30%. Nonetheless, the second a few quotes are a couple of to three times smaller than the initial a couple of. All of the rates of ? provides highest practical deviations, reflecting the fresh expected genome-greater type in recombination, and especially so for the estimate regarding sequencing study, possibly because of the much larger quantity of nucleotides inspected.