Genomic introgression mapping of field-derived multiple-anthelmintic resistance in Teladorsagia circumcincta
Fig 2
Genome-wide scan of fixation index (FST) and copy number variation (CNV) between Sinbred and RS3 populations of Teladorsagia circumcincta.
(A) Mean FST values for 1-kb sliding windows (grey) were subjected to kernel smoothing (red) to locate contiguous regions of the genome with high levels of population differentiation. Outlier regions (above the dashed line FST = 0.40 (z-score = 4.5)) were identified based on the empirical distribution of the smoothed FST values. The length and the number of genes per region (in brackets) are indicated for protein coding outlier loci. Due to the lack of information regarding the long-range relationship of the scaffold sequences, numerical index was used as the unit of relative location along the horizontal axis instead of the absolute genomic coordinates. Within each scaffold the order of windows followed the genomic coordinates. A total of ~325,000 windows were included in the analysis. (B) Total combined length of outlier regions, number of overlapping contigs and genes under different FST z-score cutoff values. (C) CNV was presented as the ratio of RS3:Sinbred normalized depth. Raw read count ratios (grey) and statistically significant CNV regions (blue). Top 10 outlier regions that contain protein-coding genes (log2 ratio >2.9; above dashed line) were identified (Table 2). The length and the number of genes per region (in brackets) were indicated. (D) FST of ddRAD-seq derived SNP markers between ivermectin-screened and drug-naïve F2 mapping populations of T. circumcincta (n = 24 for each population). Outlier loci were determined using z-score cutoff values based on the empirical distribution of FST estimates in each sampling depth category (represented as green lines of increasing intensity, ranging from a z-score of 2 to 4.5 in 0.5 increments).
