The relative orders of most duplicate loci on the homeologous chromosomes were similar.
Additionally, we selected the 100 most duplicated genes according to the average of 5 kub window coverages of the duplicated merged intervals and identified the matched InterPro domains for these genes.
Among the 100 most duplicated genes, 21 detect homologous genes in mitochondria and/or chloroplast genomes.
We performed a genome-wide comparative analysis of functional domains traced in single versus duplicated genes and also focused on the 100 most duplicated genes, which revealed two important aspects.
A few genes coding for the cytochrome P450 domain, found in plant enzymes involved in the biosynthesis of several compounds such as hormones, defensive compounds and fatty acids [ 48, 49], are among the 100 most duplicated.
Several genes among the 100 most duplicated contain functional domains with oxidoreductase activity, such as ferrodoxin, enzymes involved in the respiratory and photosynthetic electron transport chains, aldo-keto reductase, glucose/ribitol dehydrogenase, and stearoyl-acyl-carrier-protein desaturase.
The high rate of duplication of CAD genes and the retention of most duplicates raises the question of their functional redundancy.
Conclusions: The most common duplicate publication involves sequential publication of very similar data and conclusions.
The probability of X2 retaining the same copy as C is equal to the probability that X2 and C (but not X1) retain the most likely duplicate, 0.5(1+r) X 0.5(1+r) X 0.5(1−r), plus the probability that X2 and C (but not X1) retain the less likely duplicate, 0.5(1−r) X 0.5(1−r) X 0.5(1+r).
When only the most divergent duplicate genes are used for coalescence estimates, a date of 153 Mya was obtained.
