Table 1. Prophage strains used in this study.
| Prophage | Host insect | Common Name | Wp group | Wp strain | Rp | ORFs | Head/Bp | Vir./Tail | Rec. | Rep. | Unchar. | Ref |
| WOCauB2 | Cadra cautella | moth | B | wCauB | CI | B2gp1-gp47 | gp11-gp27 | gp28-gp47 | gp1-gp3 | gp4-gp10 | NA | [44] |
| WOCauB3 | B2gp1-gp46 | gp12-gp28 | gp29-gp46 | gp1-gp3 | gp4-gp11 | NA | ||||||
| WOPip1 | Culex pipiens | mosquito | B | wPip | CI | WPa_0242-0272 | WPa_0242-0261 | NA | NA | WPa_0262-0270 | WPa_0271-0272 | [29] |
| WOPip2 | WPa_0297-0322 | WPa_0301-0318 | NA | NA | WPa_0319-0322 | NA | ||||||
| WOPip3 | WPa_0323-0342 | WPa_0323-0336 | NA | WPa_0337-0342 | NA | NA | ||||||
| WOPip4 | WPa_0411-0455 | WPa_0415-0430 | WPa_0438-0455 | WPa_0411-0414 | WPa_0433-0437 | WPa_0431-0432 | ||||||
| WOPip5 | WPa_1294-1340 | WPa_1294-1311 | WPa_1321-1340 | NA | WPa_1312-1318 | WPa_1319-1320 | ||||||
| WOMelA | Drosophila melanogaster | fruit fly | A | wMel | CI | WD_0261-0288 | WD_0261-0284 | NA | WD0285-0288 | NA | NA | [30] |
| WOMelB1 | WD_0565-0610 | WD_0593-0605 | WD_0581-0565 | NA | WD_0582-0592 | WD_0606-0610 | ||||||
| WOMelB2 | WD_0634-0644 | WD_0638-0644 | NA | WD_0634-0637 | NA | NA | ||||||
| WORiA-1 | Drosophila simulans Ri. | fruit fly | A | wRi | CI | wRi_005400-005720 | wRi_005460-005650 | NA | wRi_005400-005450 | NA | wRi_005660-005720 | [43] |
| WORiA-2 | wRi_010060-010380 | wRi_010120-010310 | NA | wRi_010060-010110 | NA | wRi_010320-010380 | ||||||
| WORiB | wRi_006880-007250 | wRi_p07230-007070 | wRi_007060-006880 | wRi_p07240-007250 | NA | NA | ||||||
| WORiC | wRi_012450-012670 | wRi_012670-012470 | NA | wRi_012450-012460 | NA | NA | ||||||
| WOVitA1 | Nasonia vitripennis | jewel wasp | A | wVitA | CI | VA1gp1-gp51 | VA1gp5-gp23 | VA1gp35-gp51 | VA1gp1-gp4 | VA1gp27-gp34 | VA1gp24-gp26 | [28] |
| WOVitA2 | VA2gp1-gp39 | VA2gp9-gp31 | NA | VA2gp1-gp3 | VA2gp4-gp8 | VA2gp32-gp39 | ||||||
| WOVitA4 | VA4gp1-gp31 | VA4gp5-gp27 | NA | VA4gp1-gp4 | NA | VA4gp28-gp31 |
Wp-Wolbachia pipientis; Rp- reproductive parasitism; CI – cytoplasmic incompatibility; NA – not applicable; Bp – Baseplate; Vir. – Virulence; Rec. – Recombinase; Rep. – Replication; Unchar. – Uncharacterized. WOVitA3 was not analyzed because the initial identification via PCR product published in [45] was found to be a chimera. For the purposes of this study, WOMelB1 and WOMelB2 are combined into one haplotype, WOMelB; see text for justification. Similarly, WORiA-1 and WOiRA-2 are analyzed as one haplotype, WORiA, since they are identical copies.