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We chose both types of duplicates because: 1) tandem duplicates and retrogenes are easier to screen, and 2) after ancient large-scale genome duplications at the origin of vertebrates, most duplicates have been created via small-scale events in mammalian genomes [ 8].
The high rate of duplication of CAD genes and the retention of most duplicates raises the question of their functional redundancy.
Even if most duplicates degenerate into pseudogenes (nonfunctionalisation or pseudogenisation) within 50 million years following the duplication event, a remarkable number of gene duplicates are found in vertebrate genomes [ 16].
In addition, the non-synonymous substitutions in most duplicates are under selective constraints (dN/ dS < 1).
For all cutoffs tested, most duplicates were classified as conserved, and the relative numbers of pairs in parent and child neofunctionalization classes were similar.
In general it is observed that most duplicates tend to become subfunctionalized or pseudogenized in the absence of purifying selection [ 32].
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Among these duplicated pairs, the average Ka/Ks value of segmental duplication was very similar to those in tandem duplication (~0.4), indicating that most duplicated ZmPP genes are under strong purifying selection pressure.
One more cross-species study reports that most duplicated genes experience a short post-duplication period of relaxed neutral selection [ 12].
More details of the simulated data results can be found in Additional file 1. Figure 2 shows that CRF based methods reveal correct alignments for most duplicated nodes as well as non-duplicated nodes.
Interestingly, six of 16 gene pairs located on duplicated chromosomal segments showed differential expression patterns, suggesting that most duplicated gene pairs were under the diverse transcriptional controls.
Organ/tissue expression patterns and promoter activity assays of the soybean PINs suggested redundant functions for most duplicated genes and complementary and tissue-specific functions during development for non-duplicated genes.
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CEO of Professional Science Editing for Scientists @ prosciediting.com