Because the genomes of domestic species (except for chicken) were used as the reference genomes for mapping, and the wild species usually have lower read mapping ratios compared to the domestic species (Additional file 1: Figure S3), it is necessary to determine whether mapping bias caused by genetic differences between the genomes of domestic and wild species would reverse the pattern of decreased expression diversity. To test this, we mapped the reads of rice by using the reference genome of the wild species, O. nivara (GCA_000576065.1), and analysed the gene expression diversity of the wild and cultivated rice. The degree of decreased gene expression diversity of the cultivated species (1.054) compared to the wild species (1.205) was even higher (12.5% decrease, P < 2.2e-16) than that obtained using the genome of Oryza japonica as the reference (5.1% decrease, P < 1.1e-12) (Table 2, Additional file 1: Figure S4), indicating that a lower mapping ratio may underestimate the expression diversity of wild species and the degree of decreased expression diversity when the genome of domestic species is used. In addition, we also observed significantly lower expression diversity in the domestic chicken when using the genome of wild chicken (Gallus gallus) as the reference genome (Fig. 1a, Table 2). These results suggest that mapping ratio differences caused by reference genome difference between the domestic and wild species do not change the observed result.
Towards the eight sets, brand new candidate places one to underwent choosy sweeps throughout domestication was indeed before stated [14, 18, twenty-eight, 31,thirty two,33,34,35]. (more…)