Abstract
BackgroundDiversity-generating retroelements (DGRs) are a unique family of retroelements that generate sequence diversity of DNA to benefit their hosts by introducing variations and accelerating the evolution of target proteins. They exist widely in bacteria, archaea, phage and plasmid. However, our understanding about DGRs in natural environments was still very limited.ResultsWe developed an efficient computational algorithm to identify DGRs, and applied it to characterize DGRs in more than 80,000 sequenced bacterial genomes as well as more than 4,000 human metagenome datasets. In total, we identified 948 non-redundant DGRs, which expanded the number of known DGRs in bacterial genomes and human microbiomes by about 55%, and provided a much more comprehensive reference for the study of DGRs. Phylogenetic analysis was done for identified DGRs. The putative target genes of DGRs were searched, and the functions of these target genes were investigated with a comprehensive alignment against the nr database.ConclusionsDGR system is a powerful and universal mechanism to generate diversity. DGR evolution is closely associated with the living environment and their cassette structures. Furthermore, it may impact a wide range of functional processes in addition to receptor-binding. These results significantly improved our understanding about DGRs.
Highlights
Diversity-generating retroelements (DGRs) are a unique family of retroelements that generate sequence diversity of DNA to benefit their hosts by introducing variations and accelerating the evolution of target proteins
Compared with 610 unique known DGRs in bacterial genomes and human metagenomes, our finding expanded the number of known DGRs by about 55%
For the partial DGRs, we aligned the whole genome sequencing (WGS) raw reads to the corresponding variable repeat (VR), and we found 3,036 template repeat (TR)-VR pairs with at least two supporting reads, which resulted in 62.7% of the partial DGRs (848 of 1,353) confirmed (Additional file 15: Data 1c)
Summary
Diversity-generating retroelements (DGRs) are a unique family of retroelements that generate sequence diversity of DNA to benefit their hosts by introducing variations and accelerating the evolution of target proteins. They exist widely in bacteria, archaea, phage and plasmid. DGRs are a unique family of retroelements that generate sequence diversity of DNA They exist widely in bacteria, archaea, phage and plasmid, and benefit their hosts by introducing variations and accelerating the evolution of target proteins [1,2,3,4,5]. The first DGR was discovered in a Bordetella phage, BPP-1. The invasion of BPP-1 to Bordeltella relies on the phage tail
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