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The 30 accessions were excluded from further analysis because they constitute duplicate accessions or because genotypic composition suggests they either could be feral barley accessions or were subject to recent introgression.
This implies that only a very small proportion of the transcripts identified may constitute complementary-strand duplicates rather than single gene calls.
This region constitutes a duplicate of the previously identified IB region on chromosome 14 with the ssZBAb, ssZCAb and ss ZDAb genes.
Duplicates generally constitute a few percentage of short-insert size libraries (<500 bp), but can reach over 95% for long-insert libraries (>10 kb).
In our case, duplicate reads constitute ∼95% of all reads (because of the high depth of coverage of our data).
Here, we report that GIF1 and another CWI gene OsCIN1 constitute a pair of duplicate genes with differentiated expression and function through independent selection.
Here, we report that GIF1 and another CWI gene OsCIN1 constitute a pair of duplicate genes with differentiated expression and function.
Although these duplicates constituted a relatively modest fraction of the conserved syntenic homologs (14.5%, Fig. 3a; 18.2%, Fig. 3b; not counting redundant copies), we interpret these as strong evidence that large-scale (whole-genome) duplication has had a major role in shaping gnathostome genome architecture.
For that reason, the discovery of a fixed and long-term stable (estimated as > 100 Mya) duplication in Drosophila, as well as the rapid and heterogeneous accumulation of amino acid changes between duplicates, constitutes a very unusual feature for this family.
In this case, random SSD taking place in our WGD timing window would constitute a background level of duplicates, but we should not observe a Ks distribution peak, evidence of a unique event.
