Prokaryotic genes in eukaryotic genome sequences: when to infer horizontal gene transfer and when to suspect an actual microbe.
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.
N.I. Vavilov Institute of General Genetics RAS, Gubkina 3, Moscow, 119991, Russia.|A.A.Kharkevich Institute for Information Transmission Problems, Russian Academy of Sciences, Bol'shoy Karetny 19, Moscow, 127994, Russia.|M.V. Lomonosov Moscow State University, Faculty of Bioengineering and Bioinformatics, Vorobyevy Gory 1-73, Moscow, 119992, Russia.
Irena I
II
Artamonova
Department of Natural Sciences, Novosibirsk State University, 2 Pirogova Str., Novosibirsk-90, 630090, Russia.
Tanya
T
Lappi
St Mary's School Calne, Wiltshire, SN11 0DF, UK.
Liudmila
L
Zudina
Division of Molecular and Cellular Biosciences, National Science Foundation, 4201 Wilson Boulevard, Arlington, VA, 22230, USA.
Arcady R
AR
Mushegian
D001419:Bacteria / Q000235:genetics*; D001483:Base Sequence; D005075:Biological Evolution; D019295:Computational Biology; D004269:DNA, Bacterial / Q000235:genetics*; D056890:Eukaryota / Q000235:genetics*; D022761:Gene Transfer, Horizontal; D005798:Genes, Bacterial; D016680:Genome, Bacterial / Q000235:genetics; D010802:Phylogeny
D004269:DNA, Bacterial