Genomic correlates out-of 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.
Efficiency
The two linkage charts constructed with separate sets of SNPs contained 4396 SNPs having E. grandis and you may 3991 to own Age. urophylla, layer similar total recombination distances (Fig. 1; Dining table S1; Notes S1). A total of 192 (dos.3%) nonsyntenic SNPs, was indeed omitted, which is SNPs one to mapped so you can linkage teams unlike the newest expected of those centered on their genome status. New alignment of one’s E. grandis maps to the current genome variation step 1.1 found assembly inconsistencies on the several chromosomes, alot more somewhat into the chromosomes step one, 2, cuatro and 8 (Figs step 1, dos, S1). Map-situated rates out-of recombination costs had been similar into the several varieties, 3.18 ± step 1.1 and you will step 3.55 ± 0.8 cM Mb ?1 (Table S1). The fresh M arey maps (Figs dos, S1) found a fairly similar hill of recombination speed across every chromosomes, and only small plateaus regarding recombination have been viewed, such as for instance, into chromosomes 4, 9 and you can ten.
Extent regarding genome-wide linkage disequilibrium into the E. 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 https://datingranking.net/local-hookup/lloydminster/ 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 rate into the E. grandis
About three methods to see genome-broad rates out of ? was in fact undertaken playing with several separate fresh investigation set nearby almost thirteen million SNPs on pooled series studies as well as 21 one hundred thousand Infinium SNPs. Chromosome-certain quotes away from ? was in fact gotten a variety of genomic windows versions when it comes to SNP amounts with LDH within and you will H otspotter (Dining table step 1). Quotes was determined across all chromosomes in 2402 overlapping bins away from fifteen SNPs (mean bin dimensions, 250 kb; SNP occurrence, 1/16.seven kb) and in 242 overlapping pots off 105 SNPs (suggest container size, 2500 kb; SNP density, 1/ kb). Nothing adaptation is actually viewed among them quotes and you can across chromosomes. Quotes obtained by H otspotter was indeed overall two times as higher as the people of LDH at the , most likely highlighting various assumptions regarding the LD brand of the fresh a couple quote measures. Therefore, the genome-wide quotes out-of active population versions gotten by the equating ? to help you the newest recombination rate c had been as well as doubly highest that have H otspotter . The genome-greater rates regarding ? received with Infinium SNPs converged to really equivalent philosophy and you can magnitudes towards the guess obtained on the pooled sequencing investigation using mlRho as well as to estimates produced from population-level LD (Table dos). Even though some degree of sampling prejudice built-in with the approach appears as present when comparing the brand new quotes out-of ? away from H otspotter and you will mlRho and just have involving the prices out-of LDH during the and populace-peak LD, the values did not differ because of the > 30%. Still, aforementioned two quotes are two to 3 times smaller compared to the initial a couple of. Every rates regarding ? has actually highest standard deviations, showing the new expected genome-broad variation for the recombination, and especially so towards the guess regarding sequencing study, maybe because of the larger level of nucleotides examined.