Fig. 6

Introgressed genes falsely identified as being less expressed due to reference bias. A Mapping coverage deviation of DNA reads across chr1D of Jagger, Cadenza, and 5 of the accessions analysed by He et al. [11]. Each point is the coverage deviation value for a given 1-Mbp genomic window. Windows with a normalised coverage score significantly different to the median normalised coverage score for that window across the set of lines being compared are coloured red. Coverage deviation values significantly below one indicates divergent material is present or a deletion has taken place, relative to the median of the rest of the set of lines. Coverage deviation values and significance values were calculated separately for the accessions and for the cultivars Jagger and Cadenza, the latter two being compared to mapping coverage values from the other cultivars whose genomes were assembled as part of the 10+ wheat genomes project [20]. The reduced coverage at the end of chr1D, the left-hand border of which is indicated by the vertical dashed black line, is the chr1D introgression, common to 53 of the 198 accessions and Jagger and Cadenza which were assembled as part of the 10+ wheat genomes project. B Expression of the wheat gene compared to its introgressed orthologue from the chr1D introgression, using either Chinese Spring or the pantranscriptome reference as targets for kallisto pseudoalignment. Orthologue pairs with TPM < 1 in both the introgressed and the wheat copy when mapping to the pantranscriptome reference were excluded. The significance of the difference between introgressed and non-introgressed orthologues when using the Chinese Spring or the pantranscriptome reference was calculated using two-tailed t tests with no assumption of equal variance