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Phylogenetic discrepancies between T. crunogena SoxCD (and the highly similar Lost City SoxCD) compared to the other Sox proteins are consistent with one or more lateral gene transfer events [23].
Free-living bacteria exhibit larger genomes, more lateral gene transfer [ 13], and more rRNA operons.
Given the diversity of Hemiptera genomes and transcriptomes that encode bacterial lysozyme, including representatives from Heteroptera and Sternorrhyncha, and given the clustering of these lysozyme genes with α-proteobacterial lysozymes, the lysozyme genes in Hemiptera likely result from one or more lateral gene transfer(s) that occurred prior to the radiation of this order or its suborders.
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In analyses of sequence data for 40 genes, lineage II strains were significantly more likely to be identified as recipients of DNA fragments by horizontal gene transfer, indicating either more frequent lateral gene transfer or more frequent fixation of recombinant fragments.
Previous studies indicate a possible more ancient lateral gene transfer of fatty acid biosynthesis genes from α-proteobacteria to actinobacteria [ 84].
Could then the present result be explained either (i) by a much more ancient lateral gene transfer (somewhere at the base of the bruchids, in which case the scenarios should try to explain this ancient phenomenon) or if not, eventually (ii) by some complex scenarios of independent genes losses to explain the patchy distribution of cytb in current bruchid populations?
Mitochondria were created as a mosaic and later incorporated more elements through lateral gene transfer (LGT) or recombination events from other Alphaproteobacteria.
They are more refractory to lateral gene transfers and usually present in a single copy in genomes, which avoids recombination and issues related to divergence between copies (Case et al. 2007; Adekambi et al. 2009).
The specific relationship between the eukaryotic TK-Ch and Chlamydiales TK sequences is also difficult to reconcile with such an ancient origin, suggesting instead that the corresponding gene may have originated more recently by lateral gene transfer from an ancestor of the Chlamydiales group.
The Euglenozoa are very isolated in the tree of eukaryotes from other lineages currently known to encode EFL, and therefore EFL's origin in the Euglenozoa is more simply explained by lateral gene transfer, but the demonstration here that differential loss plays a role in EFL's distribution needs to be considered more carefully at all levels of the tree.
These differences are largely attributable to the presence of more genes associated with lateral gene transfer in SM39 such as insertion sequence (IS) transposases and integrases (category L), and genes for restriction-modification systems and multidrug transport systems (category V).
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