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In both Arabidopsis and rice, locally duplicated ohnologs are widely distributed in different duplicated chromosomal segments that cover all chromosomes (fig. 2), suggesting that local duplications of ohnologs are not specific to certain chromosomal regions.
We identified tens of cases in which paired BAC ends fell in different duplicated regions.
Locally duplicated ohnologs are widely distributed in different duplicated chromosomal segments and functionally biased.
These different outcomes likely apply to different duplicated KMT genes, judging from their expression patterns (Additional File 3: Figure S2).
In sharks, the ancestral 5S class I genes derive from different duplicated genes that originated before the separation of the Agnathans and the Gnathostomans species [ 30].
We reached the same conclusions after calculating the Ka/Ks ratio for the two different duplicated gene groups - GCO and nGCO - with respective values 0.09 and 0.43 (Fig. 2).
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We found that NE-determined cut-off value varies among different duplicate pairs, suggesting that empirical cutoff value is not suitable for every case.
For two post-duplication outgroups, the KNST branch length is e2-e1 (if both outgroups retain the same duplicate; Figure 3b,e) or 2d-e2-e1 (if different duplicates are retained; Figure 3c,d).
The total expected NST internal branch length is then equal to (i) the probability that X1 and C retain the same duplicate, 0.5(1+r2), times e1, plus (ii) the probability that X1 and C retain different duplicates, 0.5(1−r2), times the average of e2 and 2d-e2 (which is d).
However, different duplicate gene pairs might have different levels of functional similarity.
3D-JIGSAW program [ 51, 52] was used to model the 3D structure of the different duplicates.
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Justyna Jupowicz-Kozak
CEO of Professional Science Editing for Scientists @ prosciediting.com