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As the crucial feature of our simulation we further assured that indels were generated with realistic duplication characteristics as observed on the genome-wide scale (see methods).
This study investigates the duplication characteristics of the PE and PPE gene families and their association with the ESAT-6 gene clusters, using a combination of phylogenetic analyses, DNA hybridization, and comparative genomics, in order to gain insight into their evolutionary history and distribution in the genus Mycobacterium.
Thus, it is clear that the expansion of the PGRS and MPTR subfamilies was associated with a change in their duplication characteristics, and although the cause and significance of this is unknown, it may point to a corresponding change in function.
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EUD-1 emerged following a lineage-specific duplication characteristic to Pristionchus, and executes a developmental switch for morphological plasticity in the adult stage, showing that regulatory pathways can evolve by terminal addition of new genes [ 37].
Among these 29 insertions, 28 had target-site duplications characteristic L1-mediated mobilization (Fig. 1A).
In vertebrates in particular, the steroid receptor repertoire has been shaped by genome duplications characteristic to this lineage.
For this purpose, we chose the Drosophila melanogaster genome because of its relatively compact size and absence of genome wide duplications characteristic of vertebrates.
A recent study on gene family evolution dynamics (Wapinski et al 2007) showed that duplication resistant characteristics are typical for genes related to essential growth processes, genes active in organelles and nucleus, and genes essential for viability.
A search in the PEST genome with these MITE consensuses using the TE annotation pipeline identifies numerous full-length copies that are flanked by an 8 bp perfect target site duplication (TSD) characteristic of the P element family.
Duplication is characteristic of insect populations being isolated from one another while the host is not and does not imply that a duplicated lineage has to arise on the same host species nor in allopatry [ 52].
It is possible that BSP30 gene duplication is a characteristic feature of ruminants and that the BSP30 proteins contribute to an aspect of ruminant-specific physiology.
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