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.
Performance
Both linkage charts built with separate groups of SNPs contains 4396 SNPs to own Age. grandis and you may 3991 having Elizabeth. urophylla, covering similar full recombination distances (Fig. 1; Table S1; Notes S1). A total of 192 (2.3%) nonsyntenic SNPs, was basically excluded, that is SNPs you to definitely mapped so you can linkage teams distinct from this new asked of those centered on their genome status. The fresh positioning of the Elizabeth. grandis maps to the current genome type 1.step one revealed set-up inconsistencies with the multiple chromosomes, even more notably with the chromosomes step 1, dos, cuatro and you may 8 (Figs 1, dos, S1). Map-situated prices out of recombination pricing were similar towards the a couple of variety, step 3.18 ± step 1.step one and you may 3.55 ± 0.8 cM Mb ?step 1 (Desk S1). The fresh Yards arey charts (Figs 2, S1) shown a fairly equivalent slope regarding recombination rate around the all the chromosomes, and simply more compact plateaus from recombination was indeed viewed, eg, on chromosomes 4, nine and you can 10.
The quantity out-of genome-large linkage disequilibrium in Age. 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 when you look at the Age. grandis
Around three methods Badoo indir to obtain genome-greater rates away from ? was indeed undertaken using two independent experimental research establishes related almost 13 mil SNPs from the pooled succession analysis and over 21 100 Infinium SNPs. Chromosome-certain estimates out-of ? was indeed obtained for various genomic window systems when it comes to SNP wide variety which have LDH during the and you will H otspotter (Table step 1). Rates have been calculated all over all the chromosomes during the 2402 overlapping containers out-of fifteen SNPs (mean container size, 250 kb; SNP thickness, 1/sixteen.seven kb) and also in 242 overlapping containers of 105 SNPs (mean container dimensions, 2500 kb; SNP thickness, 1/ kb). Absolutely nothing type are seen between them quotes and you can across chromosomes. Prices acquired from the H otspotter had been as a whole doubly highest as those people out-of LDH at , probably reflecting the many assumptions about your LD model of the brand new a couple estimate actions. Therefore, the newest genome-wide rates out of active people brands gotten because of the equating ? so you can the recombination rates c had been in addition to two times as higher with H otspotter . The fresh genome-large rates away from ? obtained which have Infinium SNPs converged to really similar philosophy and magnitudes with the imagine obtained towards the pooled sequencing research having fun with mlRho as well as to estimates based on population-peak LD (Table 2). While some degree of testing bias built-in towards means seems to get establish when you compare the fresh new prices away from ? off H otspotter and you may mlRho and just have amongst the rates away from LDH from the and you will populace-top LD, the prices didn’t differ of the > 30%. However, the latter a couple prices are two to 3 moments smaller compared to the first a couple of. Most of the rates out-of ? has actually high practical deviations, reflecting this new expected genome-greater type within the recombination, and especially very towards the imagine away from sequencing investigation, perhaps as a result of the bigger level of nucleotides examined.