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Indeed, our study finds six yeast proteins (all complex II subunits, Qcr6p and Cox5p), whose duplication is mapped to the WGD event.
The analysis of the flanking gene families revealed that those which are multi-copy and whose duplication timing coincides with vertebrate emergence, typically have their members localizing to Hsa4, Hsa5, Hsa8, Hsa10 and/or Hsa2.
To further exploit our CGH and transcriptomic data, we focused on small-scale rearrangements that might help us pinpoint candidate genes whose duplication, deletion or breakage might be involved in tumorigenesis.
The only large repeat (> 100 bp) that can be identified from the genome is a 1200 bp fragment encoding the elongation factor Tu gene, whose duplication is known to be widespread among proteobacteria [ 17].
All indel mutants occurred in a 102 base pair region within exon 14 of the FLT3 gene, except for one case (0126) whose duplication included one base in the intronic region between exon 14 and 15.
One intriguing hypothesis is that genes whose duplication and recruitment have been useful to meet current Darwinian challenges find themselves in regions of the chromosome that favor the generation of LCRs.
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The gene families whose duplications coincide with the 2R-WGD show a dense pattern of gene-by-gene paralogy among the identified regions on chromosomes 1, 4, 5, and 6 (fig. 4).
It appears that these two classes of proteins are exceptional: the former are subunits of stoichiometric complexes whose duplications is discourage by selection due to the deleterious effects of imbalance [ 26], whereas the former are adaptive linear specific expansions of paralogous families evolving under positive selection [ 30].
The bias is true both for genes with a retained duplicate from the whole genome duplication, and singletons whose duplicate copies have been deleted.
First, searches of the trace server archives failed to find additional sequences whose high duplication content confounds assembly.
When the genomic status of the same 6 genes was examined in the genomes of paleopolyploids such as maize and soybean, whose genome duplication is about 10 million years old [ 33, 34], only a subset of these genes was retained as duplicates (Table 2).
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