A hidden reservoir of integrative elements is the major source of recently acquired foreign genes and ORFans in archaeal and bacterial genomes

摘要

ABSTRACT: BACKGROUND: Archaeal and bacterial genomes contain a number of genes of foreign origin that arise from recent horizontal gene transfer, but the role of integrative elements (IE) such as viruses, plasmids, and transposable elements, in this process has not been extensively quantified. Moreover, it is not known whether IE play an important role in the origin of ORFans (ORFs without matches in current sequence databases), whose proportion remains stable despite the growing number of complete sequenced genomes. RESULTS: We have performed a large-scale survey of potential recently acquired IE in 119 archaeal and bacterial genomes. We developed an accurate in silico Markov-model based strategy to identify clusters of genes that show atypical sequence composition (Clusters of Atypical Genes or CAGs) and are thus likely recently integrated foreign elements, including IE. Our method identified a high number of new CAGs. Probabilistic analysis of gene content indicates that 56% of these new CAGs are likely IE, whereas only 7% likely originated via HGT from distant cellular sources. 34% of CAGs remain unassigned, what may reflect a still poor sampling of IE associated to bacterial and archaeal diversity. Moreover, our study contributes to the issue of the origin of ORFans, because 39% of these are found inside CAGs, many of which likely represent recently acquired IE. CONCLUSIONS: Our results strongly indicate that archaeal and bacterial genomes contain an impressive proportion of recently acquired foreign genes (including ORFans) coming from a still largely unexplored reservoir of integrative elements.