In Additional file 1: Table S7, we reported that there are about 69% and 63% R-genes on average organized in clusters in monocots and eudicots respectively, suggesting that R-genes families expanded by lineage-specific tandem duplications leading to duplicated gene copy variants associated with high sequence similarities.
Although the latter induce changes in duplicated sequences, the former affect "ancestral" sequences close to duplicated loci.
Only few pseudogenes correspond to duplicated gene copies formed by the ancestral whole-genome duplication common to C. glabrata and S. cerevisiae [ 44].
Most of the pseudogenes correspond to duplicated gene copies, illustrating the extensive dynamics of gene duplications in the yeast genomes, most probably segmental duplications, as observed in S. cerevisiae [ 48].
This was partially due to duplicated genes, both tandem and segmental, more frequently having cis-eQTLs (eQTLs located at their physical positions) (Figure 3B).
83.6% of all 15 bp SAGE tag sequences could be mapped to a single location in the 12 Mbp "giardia14" genome assembly, with an additional 9.0% mapping to multiple locations primarily due to duplicated genes.
The approach applied in DIVERGE was developed for the analysis of the functional divergence of duplicated genes which, from an evolutionary perspective, we assume also applies to duplicated exons.
*Data not included in pooled means due to duplicated data.
There were 13.5 25.0% CNVRs mapped to duplicated sequences in the previous reports [ 28, 37].
Therefore with regard to duplicated genes (especially tandemly arrayed genes and (near- identical genear- identicalpondingenes alignmenthewere renamed.
The coexpression could also be due to duplicated genes, which often remain adjacent and have similarexpression patterns [ 18].
