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The orthologous contig comparison secondary peak is in the same time frame as the ortholog/paralog duplication peak.
After correcting the duplication peak medians with the appropriate ratio, we find that the youngest peak in Arabidopsis, At-α, is centered at Ks = 0.34, after the divergence of the Brassicaceae and Cleomaceae.
Genes of biological process categories that are under-represented within the genome duplication peak are "protein biosynthesis", "organelle organization and biogenesis", "cytoskeleton organization and biogenesis" and "cytoplasm organization and biogenesis".
Bayesian phylogenetic trees for the 106 arachnid gene families with a mygalomorph homolog, a scorpion homolog, and a paralog pair with a duplication node assigned to the older duplication peak tended to have low support for determining relative branching order of speciation and duplication nodes.
Similar(56)
(15) In 2D NMR spectra, misalignment often results in the duplication of peaks in the back-scaled loadings or attenuation of loading coefficients due to peak position differences and can result in compound misidentification.
In general, there is a notable tendency for very young exon duplications, with a peak appearing in the Ks distributions for all species at the interval 0.00 0.10, for ΨEs and for duplicated exons in general.
The origin of most paralogous gene families in the rice genome seems to be very old, but duplicates have continued to arise at a fairly steady pace, with a peak in duplication being coincident with a major segmental duplication that took place at ~70 MYA.
Chromosome 2 has no detectable internal segmental duplications by our analysis, and therefore has the cleanest duplication plot, with the peak centered on 0 representing tandem duplications.
The distributions of the mean d S of duplication nodes revealed two peaks in all sets, no matter the taxonomic inclusion: One peak with d S < 0.05, which probably represents recent duplications of individual genes, and a second peak at dS ∼ 0.50 with an observable valley between the two peaks (fig. 4).
Their approach complements a much more widely used approach of examining the distribution of duplications ages for peaks at different points in time (e.g. [ 66]).
Peak heights were normalized, and a deletion or duplication was identified when the normalized peak ratio value was below 0.75 or above 1.30.
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