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. Continue reading “Linkage chart positioning towards Elizabeth. grandis genome and you may map-oriented quotes of recombination”