Prokaryotic genes in eukaryotic genome sequences: when to infer horizontal gene transfer and when to suspect an actual microbeстатья
Статья опубликована в высокорейтинговом журнале
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Дата последнего поиска статьи во внешних источниках: 13 ноября 2015 г.
Аннотация:Assessment of phylogenetic positions of predicted gene and protein sequences is a
routine step in any genome project, useful for validating the species' taxonomic
position and for evaluating hypotheses about genome evolution and function.
Several recent eukaryotic genome projects have reported multiple gene sequences
that were much more similar to homologues in bacteria than to any eukaryotic
sequence. In the spirit of the times, horizontal gene transfer from bacteria to
eukaryotes has been invoked in some of these cases. Here, we show, using
comparative sequence analysis, that some of those bacteria-like genes indeed
appear likely to have been horizontally transferred from bacteria to eukaryotes.
In other cases, however, the evidence strongly indicates that the eukaryotic DNA
sequenced in the genome project contains a sample of non-integrated DNA from the
actual bacteria, possibly providing a window into the host microbiome. Recent
literature suggests also that common reagents, kits and laboratory equipment may
be systematically contaminated with bacterial DNA, which appears to be sampled by
metagenome projects non-specifically. We review several bioinformatic criteria
that help to distinguish putative horizontal gene transfers from the admixture of
genes from autonomously replicating bacteria in their hosts' genome databases or
from the reagent contamination.