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An alternative hypothesis to concerted evolution of the WD40 sequences would be a recent duplication of the genes in Podospora or a closely related ancestor.
The second comprised two rice genes (OsFTL2 and OsFTL3) that are arranged in tandem and are likely to be a recent duplication so that both can be regarded as orthologues of HvFT1 and BdFTL2.
The two Daphnia homologs cluster together and thus appear to be a recent duplication independent of that producing the two GFI homologs in humans.
When two independently indentified differentially expressed sequences clustered in the assembly in the same contig, it was assumed to be a recent duplication.
CRISPR2 and CRISPR3 from Xcaw12879 are identical except for a G at the beginning of CRISPR2, indicating that it might be a recent duplication.
The APC7 gene is also not found in the yeasts, and it could mean that it is not required for APC function in unicellular organisms and it could be a recent duplication of another TPR subunit.
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Homologs of PAB3 are present only in Arabidopsis lyrata, Capsella rubella, and Brassica rapa, suggesting that PAB3 is a recent duplication of PAB5 in the Brassicaceae.
As with PAB3, PAB8 appears only in the Brassicaceae, indicating it is a recent duplication of PAB2 to which it shares the highest degree of similarity.
For example, PAB8 is most similar to PAB2 and species containing class II PAB8-like genes are limited to A. lyrata, T. halophila, and B. rapa, suggesting that PAB8 is a recent duplication of PAB2 in the Brassicaceae.
Genes matching barley CslF10, 11, 12 and 13 [ 46] are also absent, but there appears to have been a recent duplication of the CslF3 gene in Setaria with two copies arranged as a tandem repeat on chromosome 2 (Additional file 2: Table S1).
One of these pairs, (220350/273922) shares an identity of 99% and appears to be a recent gene duplication event.
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