Linkage chart alignment towards Age. grandis genome and map-centered rates from recombination
Genomic correlates 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.
Efficiency
The two linkage charts constructed with independent sets of SNPs contained 4396 SNPs to own E. grandis and 3991 to own Elizabeth. urophylla, layer similar complete recombination distances (Fig. 1; Desk S1; Notes S1). A maximum of 192 (2.3%) nonsyntenic SNPs, was indeed omitted, that is SNPs you to mapped to linkage groups distinctive from the newest requested of them considering their genome best hookup apps Glasgow standing. The brand new alignment of one’s Age. grandis maps to the present genome type step one.step 1 revealed set-up inconsistencies to your several chromosomes, much more somewhat on chromosomes step one, 2, 4 and you can 8 (Figs step 1, dos, S1). Map-established rates from recombination costs had been comparable into one or two varieties, step three.18 ± step 1.1 and you can step three.55 ± 0.8 cM Mb ?step one (Table S1). New Yards arey maps (Figs dos, S1) found a pretty similar mountain regarding recombination rate round the the chromosomes, and only smaller plateaus regarding recombination was viewed, eg, with the chromosomes 4, nine and you will 10.
Extent regarding genome-broad linkage disequilibrium inside 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 rates in Age. grandis
Around three answers to receive genome-broad rates of ? was in fact undertaken playing with several independent fresh data kits encompassing almost 13 mil SNPs on pooled succession research as well as over 21 100000 Infinium SNPs. Chromosome-particular estimates from ? was in fact acquired for several genomic windows types when it comes to SNP number that have LDH on and you can H otspotter (Table 1). Quotes was in fact computed across all of the chromosomes when you look at the 2402 overlapping pots regarding fifteen SNPs (mean container proportions, 250 kb; SNP density, 1/sixteen.7 kb) plus 242 overlapping bins off 105 SNPs (suggest container proportions, 2500 kb; SNP thickness, 1/ kb). Little version are viewed among them quotes and you will across chromosomes. Rates obtained from the H otspotter was generally speaking doubly higher since the individuals out-of LDH at the , most likely highlighting various assumptions concerning your LD model of this new one or two quote procedures. Consequently, this new genome-broad quotes off active inhabitants systems received because of the equating ? to the fresh new recombination rate c was basically together with twice as highest that have H otspotter . The genome-wide estimates out of ? acquired with Infinium SNPs converged to really comparable beliefs and magnitudes toward imagine obtained into the pooled sequencing analysis playing with mlRho and to estimates based on population-peak LD (Dining table 2). While some amount of testing bias intrinsic on the method looks is expose when you compare the fresh new prices off ? out of H otspotter and you can mlRho and have amongst the prices of LDH at the and you may population-height LD, the prices don’t differ by > 30%. Still, the latter one or two rates are two to three moments smaller compared to the initial a couple. Most of the prices out-of ? has higher practical deviations, showing the latest envisioned genome-large adaptation within the recombination, and especially very to your estimate off sequencing research, maybe considering the larger amount of nucleotides examined.