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The fact that there is substantial ambiguity in the dating of the duplicates in duplicated segments suggests that the most recent large-scale duplication event reported here for Vitis might have occurred in close proximity to the Vitis speciation event.
Another interesting observation is that CTLDcp genes were either duplicated, or retained after a large-scale duplication, in a pronounced selective manner.
Accordingly, we used the lamprey genome to search for a signature of large-scale duplication that does not rely on the retention of duplicated genes but can be informed by their presence.
Through comparative genomics, we could find evidence that mkrn2 and mkrn4 have been duplicated together with other genes through a large-scale duplication.
We propose that the identified segmentally duplicated gene pairs were mostly conserved after the large-scale duplication event of each species during its evolution.
We also show that CTLDcp-encoding genes are selectively duplicated in Fugu, in a manner that suggests an ancient large-scale duplication event in fish.
We show that CTLDcp-encoding genes are selectively duplicated in Fugu, in a manner that suggests an ancient large-scale duplication event.
Such patterns are consistent with large-scale duplication followed by random loss of either paralogous copy.
Different approaches were taken to estimate the age of the youngest large-scale duplication event.
The age distribution of Vitis duplicates shows a clear peak of KS values between 0.6 and 1.2 suggesting a relatively recent large-scale duplication event (Figure 7D).
We also observed frequent duplication of ESAGs, including a large-scale duplication in BES1 (Tan40), an ESAG7 triplication in BES4/TAR28 and three cases of divergent additional copies of ESAG8 (BES13 BES13 and BES15).
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