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Similar duplicate genes dating to these genome duplications are called '2R-ohnologues' or 2R-paralogues [ 40].
The large amount of highly similar duplicate sequences caused by the relatively recent genome duplication in the salmonid ancestor represents a particular challenge for the genome project.
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This feature eliminated very similar (duplicate) channels.
By removing highly similar duplicate pairs, we remove those duplicates that are most likely to be problematic for MultiLoc2.
To minimize potential biases introduced by homology, we reanalyzed the data by first removing all highly similar duplicate pairs (Ks < 0.01).
Similar(49)
Total counts of duplications were also computed discarding the fraction of duplications that is expected to be more sensitive to error annotation: lineage-specific duplications with highly similar duplicates and duplications found in recently assembled genomes (see main text).
This result is expected because only very similar duplicates should exhibit off-target cross-reaction.
Such highly similar duplicates could be recovered with reasonable success by aCGH.
The O. pardalina hsp70 pseudogenes likely arose by retroposition, as suggested for similar duplicated hsp70 genes and pseudogenes in Drosophila [ 22, 23].
Morrow et al., who identified the two intronless RH1 genes in the zebrafish genome, also identified similar duplicated genes in a few other cyprinid species [ 41].
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