- Bordetella phage BPP-1 [see myDGR prediction]
The prototypical diversity-generating retroelement (DGR) was discovered in a Bordetella phage BPP-1. The myDGR server predicts a DGR system on the reverse strand of the genome. The DGR system found in Bordetella phage genome was shown to mediate the phage tropism specificity by generating variability in the target gene (mtd), resulting in massive sequence variation in the phage’s receptor-binding protein Mtd encoded by the target gene.
Ref: Tropism switching in Bordetella bacteriophage defines a family of diversity-generating retroelements (paper)
- Treponema denticola [see myDGR prediction]
Treponema denticola is a Gram-negative, obligate anaerobic bacterium, which lives in the oral cavity and is highly specialized to survive in this environment. T. denticola is associated with the incidence and severity of human periodontal disease. T. denticola has eight target genes subject to the DGR system in its genome; one is in the core DGR, and the rest scatter across the genome. For four out of the eight target genes, putative GC-rich repeats (forming a hairpin) were found in their downstream.
Ref 1: Genomic and Metagenomic Analysis of Diversity-Generating Retroelements Associated with Treponema denticola (paper)
Ref 2: Conservation of the C-type lectin fold for massive sequence variation in a Treponema diversity-generating retroelement (paper)
- Stenotrophomonas sp. SKA14 [see myDGR prediction]
Stenotrophomonas sp. SKA14 belongs to Gammaproteobacteria. Interestingly, its DGR has eight target genes in tendem.
- Archaeon GW2011_AR20 [see myDGR prediction]
Archaeon GW2011_AR20 was assembled from a groundwater metagenome (ncbi). This genome has multiple target genes that are putatively subject to the diversification by DGR system. All the VR regions are relatively short (about 70bps) compared to the DGRs found for example in Bordetella phage and T. denticola genomes. Since myDGR did not find similarity between the protein sequences encoded by the genes close to the RT gene and previously identified accessory genes, it didn't report accessory gene; instead, it outputs all four genes nearby the RT gene for users to check out.
Ref: Retroelement-guided protein diversification abounds in vast lineages of Bacteria and Archaea (paper)
- Bacteroides dorei Hankyphage [see myDGR prediction]
Bacteroides dorei Hankyphage was found to contain a DGR system. This phage lysogenizes 13 different Bacteroides species and was present in 34% and 21% of whole-community metagenomes and human-associated viromes, respectively as reported in this paper.
Ref: A diversity-generating retroelement encoded by a globally ubiquitous Bacteroides phage (paper)
- Nostoc sp. PCC 7120 [see myDGR prediction]
The genome of this filamentous nitrogen-fixing cyanobacterium (ref) has two DGR systems, each coming with its core components including RT gene and TR/VR pair. One DGR has a single target gene, and the other one contains a close target gene and a remote target gene.
- Candidatus Accumulibacter [see myDGR prediction]
Candidatus Accumulibacter phosphatis clade IIA str. UW-1 has two DGR systems , each having two target genes.