The system proposed by Irina Arkhipova assigns all mobile genetic elements a code based upon the origin of three important components: the component responsible for their copy number increase (Polymerizing), the component responsible for their integration back into the genome (Integrative), and any structural components they might possess. This also captures the modularity of mobile genetic elements, and their interconnectivity across the Tree of Life and with other entities such as plasmids and viruses.
| DOI | https://doi.org/10.1186/s13100-017-0103-2 |
|---|---|
| Type | Classification Schema |
| Polymerizing Component | Integrative Component | Structural Component |
|---|---|---|
| Reverse Transcriptase (R) | Serine Recombinase (S) | Envelope (E) |
| DNA Replication (D) | DDE/D Transposase (D) | Nucleocapsid (N) |
| Polymerase B (B) | Tyrosine Recombinase (Y) | DJR capsid (J) |
| Apurinic/Apyrimidinic Endonuclease (A) | Nothing (O) | |
| PD-(D/E)XK Endonuclease (P) | ||
| GIY-YIG Endonuclease (G) | ||
| HNH Endonuclease (N) | ||
| Cas1 Endonuclease (C) | ||
| HuH Endonuclease (H) | ||
| LAGLIDADG Endonuclease (L) | ||
| Nothing (O) |
| Code | Example Elements |
|---|---|
| DS | IS607, Tn5397 |
| RD | LTR Elements |
| DD | DDE/D Elements |
| BDJ | Polinton/Maverick, Teratorn |
| RYN | DIRS-like Elements |
| DY | Crypton, Integron, CTnDOT |
| RAN | L1, RTE, CR1, L2, R1, Tad, Jockey, I |
| R(A/P)N | Dualen |
| RPN | CRE, R2, NeSL, R4, Utopia, R5 |
| DP | Restriction Endonucleases |
| RG | Penelope-like Elements |
| DG | Group I Introns, some Inteins and Homing Endonuclease Genes |
| RN | Group II Introns |
| DN | Group I Introns, some Inteins and Homing Endonuclease Genes |
| RC | RT-Cas1 |
| BC | Casposon |
| BH | Casposon |
| RH | Terminon |
| DH | Helitron, IS200/605, IS91 |
| RO | Retrons, Retroplasmids, Penelope-like Elements |
| BOJ | Linear Plasmids, Podoviridae, Tectiviridae, Adenoviridae, Megavirales |
| DL | Group I Introns, Group II Introns and Inteins |
| RL | Group I Introns, Group II Introns |