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Generally, duplicated genes that undergo divergent evolution display a tree in which the orthologues cluster and are monophyletic.
The homologs of the bacterial TSA and TSB genes are generally duplicated, e.g. the Arabidopsis thaliana genome contains two putative TSA and four putative TSB genes.
Most of the members in this "tool kit" have generally duplicated and expanded into multi-member-containing gene families with divergent functions in modern land plants [ 1, 5, 6].
De novo methods do not need a set of reference sequences to works: they used various approaches relying on the structural properties of the transposable elements as the presence of terminal repeats or the fact that transposons are generally duplicated in multiple copies in a given genome.
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Generally, processors are duplicated in parallel at stages.
The correlations between maximum indel lengths and nucleotide substitution rates are generally trivial, perhaps because duplicated genes losing long coding segments are preferentially lost following duplication.
Duplicated genes generally either disappear by accumulation of mutations (nonfunctionalization), or are preserved either by the origin of positively selected functions in one or both duplicates (neofunctionalization), or by the partitioning of original gene subfunctions between the duplicates (subfunctionalization).
While functional redundancy of homologs within a species exists (e.g. due to gene dosage requirements), it is generally believed that most duplicated genes carry out different functions [ 29- 32], though the difference has recently been shown to be relatively modest [ 33].
The ΨEs also demonstrate species-specific over-representation of GO functional categories relative to duplicated exons in general; for example, in human, GO functional categories for 'ion-binding' and 'nucleic acid binding' are significantly over-represented, compared to duplicated exons generally.
It is generally thought that the duplicated genes may undergo divergent fates during subsequent evolution such as nonfunctionalization (loss of original functions), neofunctionalization (acquisition of novel functions), or subfunctionalization (partition of original functions), which may be indicated by divergence in their expression patterns [ 60, 61].
They are generally in duplicate, suggesting a very ancient duplication of this gene in fungi by a clearly distinct process from the acquisition of the cluster.
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