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It is noteworthy that MCPs in A. fischeri ES114 tend to be duplicated in tandem repeats.
However, other zebrafish Ugt1 a and b variable exons seem to be duplicated in tandem because neighboring ones are more similar to each other.
The four zebrafish Ugt2a variable exons appear to be duplicated in tandem, with the Ugt2 anda4duplicatedcated most recently (Additional file 11).
For example, PsBZPc24 to PsBZPc28 appeared to be duplicated in tandem within scaffold_15, and additional duplicates appear to have been translocated to scaffold_20 (PsBZPc31) and scaffold_8 (PsBZPc10) (assuming the apparent translocations do not result from sequence assembly errors).
Thus, the ancestral (and unique) gene encoding this clade was duplicated during the 1R-WGD, one of the two copies went on to be duplicated in tandem before the occurrence of the 2R-WGD.
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Prior to duplication, this locus was duplicated in tandem; after duplication, one copy was lost from chromosome 8 and another is currently being deleted from chromosome 4, thereby restoring the original copy number.
We observed three distinct patterns of duplication events for B3 genes according to their duplication origin: genes that were duplicated and inserted in different chromosomes, genes that were duplicated and inserted in the same chromosome and genes that were duplicated in tandem.
Even more may be possible for loci involving genes that are duplicated in tandem repeats or loose clusters [ 14].
So they may have been identified by the enrichment methods because they are duplicated in tandem and not because they could be involved in the trait variation.
In conjunction with the clustered genomic organization (Fig. 1), the tree demonstrates that variable exons of the Ugt1 clusters are duplicated in tandem.
On the other hand, we found that most of tandem duplication occurred by a one-gene mode, i.e. only one gene was duplicated in a one tandem duplication event as shown in Figure 6.
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