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Moreover, Eurotatoria appeared paraphyletic in previous analyses comprising several monogononts [ 17, 19] which cannot be explained by long-branch attraction due to an accelerated sequence evolution in B. plicatilis.
HGT, complex gene duplication events and an accelerated sequence divergence may mask the discovery of orthologs, making comparative studies of TRN a particularly difficult task; see Box 2. Before any biological question about TRNs can be asked, the technical problem of obtaining a reliable network must be solved.
The majority of the imprinted genes in Wolff et al. (2011) have a restricted expression pattern and an accelerated sequence evolution rate compared with their paralogs; however, although this trend is found in imprinted genes in Hsieh et al. (2011), it is less obvious than in the genes from Wolff et al. (2011).
However, since a high signal-to-noise ratio (SNR) is essential to probe the differences in tangentiality between the different laminae, this would need an increase in scanning time or application of an accelerated sequence in order to achieve the same SNR.
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Gene duplication is often followed by a period of accelerated sequence evolution in one or both gene copies [10] [12].
In addition, I investigate if either paralog is equally likely to embark on a trajectory of accelerated sequence evolution or whether the derived paralog is more likely to exhibit faster sequence evolution.
Thus, imprinted genes and their paralogs have a higher frequency of accelerated sequence evolution than gene pairs as a whole that were duplicated by the alpha WGD.
These results precluded a role for positive selection (i.e., when a duplication was followed by accelerated sequence divergence) as the explanation for all 5 paralogs having bidirectional promoters with unrelated partner genes.
Several unusual features were found: retention of the ATP synthase genes and rbcL gene; extensive gene order rearrangement despite a relative lack of repeat sequences; an unusually short inverted repeat region that excludes most of the rDNA operon; and a lack of evidence for accelerated sequence evolution.
Are a disproportionately larger fraction of such gene copies with molecular signatures of accelerated sequence evolution likely to endure a fate of extinction/pseudogenization?
These considerations motivated us to perform a systematic genome-wide search for signatures of accelerated sequence evolution and functional innovation in noncoding sequences associated with duplicated genes.
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