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Using data from Massively Parallel Signature Sequencing, we show that a significant portion of the duplicated genes in rice show divergent expression although a correlation between sequence divergence and correlation of expression could be seen in very young genes.
We determine the relationship between sequence divergence and Bayesian phylogenetic reconstruction ability using both natural and simulated datasets.
We found a strong positive correlation between sequence divergence and physical distance.
Remarkably, we found a direct association between sequence divergence and CTCF binding divergence.
PRDM genes show an inverse relationship between sequence divergence and expression level.
However, beyond a binary assignment, a more descriptive relationship between sequence divergence and hybridization ratio is possible.
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After investigating the frequency of asymmetric rate evolution for those duplicates with reciprocal expression, we conducted an analysis to see if there is any association between asymmetric sequence divergence and expression divergence.
A strong correlation between sequence divergence in these lag genes and sorting during fruiting body formation supports the hypothesis that these genes are important in kin discrimination.
In the seven remaining species however, no significant correlation was found between sequence divergence, as measured by aAAI, and the percent of genes lost (see supplementary table S5, Supplementary Material online).
We analysed the relationship between amino acid sequence divergence and variation in GC3, to test the effect of evolutionary divergence on codon usage.
Essentially, the positive correlation between levels of sequence divergence and the time since the existence of a common ancestor allows us to use sequence divergence as a "molecular clock" (King and Jukes 1969; Zuckerkandl 1972).
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between mtDNA divergence and
between sequence structure and
between proteome divergence and
between sequence evolution and
between sequence depth and
between gene divergence and
between trait divergence and
between sequence conservation and
between sequence variability and
between sequence length and
between expression divergence and
between protein divergence and
between sequence identity and
between sequence similarity and
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