Table 2.
Conservation of gene content, synteny and sequence similarity in the sr1WO group Wolbachia phage, and gene-content inventory for the three sr1WOdamA1 Wolbachia phage contigs generated and characterized in this study.
| Gene name† | sr1WOdamA1 contig #1 KY695239§ | sr1WOdamA1 contig #2 KY695240§ | sr1WOdamA1 contig #3 KY695241§ | WOcauB2 AB478515‡ Coordinates Similarity (percent) Divergence (percent) BLAST score | WOcauB3 AB478516‡ Coordinates Similarity (percent) Divergence (percent) BLAST score | WOvitA HQ906663‡ Coordinates Similarity (percent) Divergence (percent) BLAST score | WOsimwRi CP001391‡ Coordinates Similarity (percent) Divergence (percent) BLAST score |
|---|---|---|---|---|---|---|---|
| WOB2pgp1 | 34–1,565 | – | – | 20,032–21,575 | 16,816–18,347 | 89–1,632 | 81,7,261–81,8794 |
| Recombinase | 1,346/1,550 (87%) | 1,318/1,538 (86%) | 1,350/1,550 (87%)* | 1,31,4/1,540 (85%) | |||
| 24/1,550 (1%) | 24/1,538 (1%) | 24/1,550 (1%) | 24/1,540 (1%) | ||||
| 1,633 bits (2,056) | 1,551 bits (1,952) | 1,649 bits (2,076)* | 1,530 bits (1,926) | ||||
| WOB2pgp2 | 1,906–3,104 | – | – | 21,893–23,090 | 18,700–19,897 | 1,950–3,1,47 | 819,117–820,31,3 |
| 1,112/1,201 (93%) | 1,108/1,201 (92%) | 1,118/1,201 (93%) | 1,132/1,200 (94%)* | ||||
| 5/1,201 (0.4%) | 5/1,201 (0.4%) | 5/1,201 (0.4%) | 5/1,200 (0.4%) | ||||
| 1,551 bits (1,952) | 1,535 bits (1,932) | 1,574 bits (1,982) | 1,632 bits (2,054)* | ||||
| WOB2pgp3 | 3,070–4,179 | – | – | 23,056–24,1,65 | 19,863–20,972 | 3,1,13–4,222 | 820,279–821,388 |
| 1,055/1,110 (95%) | 1,058/1,110 (95%) | 1,087/1,110 (98%)* | 1,034/1,110 (93%) | ||||
| 0/1,110 (0%) | 0/1,110 (0%) | 0/1,110 (0%) | 0/1,110 (0%) | ||||
| 1,544 bits (1,944) | 1,557 bits (1,960) | 1,671 bits (2,104)* | 1,462bits (1,840) | ||||
| WOB2pgp4 | 4,185–6,205 | – | – | 24,191–26,187 | 20,998–22,994 | 4,228–6,238 | 821,402–823,408 |
| 1,882/1,998 (94%) | 1,899/1,998 (95%) | 1,903/2,012 (95%) | 1,867/2,011 (93%) | ||||
| 4/1,998 (0.2%) | 4/1,998 (0.2%) | 4/2,012 (0.2%) | 11/2,011 (0.5%) | ||||
| 2,709 bits (3,412) | 2,776 bits (3,496) | 2,758 bits (3,474) | 2,612 bits (3,290) | ||||
| WOB2pgp5 | 6,211–7,441 | – | – | 26,222–27,448 | 23,029–24,255 | 6,273–7,499 | 823,443–824,669 |
| 1,190/1,233 (97%) | 1,166/1,233 (95%) | 1,191/1,233 (97%)* | 1,180/1,233 (96%) | ||||
| 8/1,233 (0.6%) | 8/1,233 (0.6%) | 8/1,233 (0.6%) | 8/1,233 (0.6%) | ||||
| 1,781 bits (2242) | 1,686 bits (21,22) | 1,785 bits (2248)* | 1,741 bits (2,192) | ||||
| WOB2pgp6 | 7,438–7,926 | – | – | 27,445–27,933 | 24,252–24,731 | 7,496–7,984 | 824,705–825,166 |
| 459/489 (94%) | 463/489 (95%) | 461/489 (94%) | 364/462 (79%) | ||||
| 0/489 (0%) | 9/489 (2%) | 0/489 (0%) | 1,2/462 (3%) | ||||
| 659 bits (828) | 667 bits (838) | 667 bits (838) | 337 bits (422) | ||||
| WOB2pgp7 | 7,950–8,745 | – | – | 27,957–28,754 | 25,283–26,023 | 8,008–8,805 | 825,190–825,987 |
| 771/798 (97%) | 625/744 (84%) | 771/798 (97%)* | 753/799 (94%) | ||||
| 2/798 (0.3%) | 11/744 (1,.5%) | 2/798 (0.3%) | 4/799 (0.5%) | ||||
| 1,159 bits (1,458) | 702 bits (882) | 1,159 bits (1,458)* | 1,084 bits (1,364) | ||||
| WOB2pgp8 | 8,797–9,288 | – | – | 28,806–29,297 | 25,537–26,021 | 8,857–9,348 | 826,039–826,530 |
| 460/493 (93%) | 448/486 (92%) | 465/493 (94%) | 475/492 (97%)* | ||||
| 2/493 (0.4%) | 2/486 (0.4%) | 2/493 (0.4%) | 0/492 (0%) | ||||
| 651 bits (818) | 621 bits (780) | 671 bits (844) | 714 bits (898)* | ||||
| WOB2pgp9 | 9,336–9,493 | – | – | 29,343–29,501 | 26,071–26,220 | 9,394–9,552 | 826,578–826,727 |
| 150/159 (94%) | 144/150 (96%) | 151/159 (95%) | 148/150 (99%)* | ||||
| 1/159 (0.6%) | 1/150 (0.7%) | 1/159 (0.6%) | 1/150 (0.7%) | ||||
| 218 bits (272) | 214 bits (268) | 221 bits (276) | 230 bits (288)* | ||||
| WOB2pgp10 | 9,642–9,799 | – | – | 29,650–29,713 | 26,370–26,430 | 9,701–9,764 | 826,877–826,937 |
| 63/64 (98%) | 61/61 (100%) | 63/64 (98%) | 60/61 (98%) | ||||
| 0/64 (0%) | 0/61 (0%) | 0/64 (0%) | 0/61 (0%) | ||||
| 99.1 bits (122) | 99.1 bits (122) | 99.1 bits (122) | 94.3 bits (116) | ||||
| 29,647–29,814 | 26,367–26,534 | 9,698–9,865 | 826,874–827,041 | ||||
| 155/168 (92%) | 155/168 (92%) | 154/168 (92%) | 154/168 (92%) | ||||
| 7/168 (4%) | 7/168 (4%) | 7/168 (4%) | 7/168 (4%) | ||||
| 211 bits (264) | 211 bits (264) | 206 bits (258) | 206 bits (258) | ||||
| WOB2pgp11 | 10,128–10,594 | – | – | 30,170–30,639 | 26,891–27,351 | 10,222–10,691 | 827,414–827,883 |
| 439/470 (93%) | 431/470 (92%) | 438/470 (93%) | 444/471 (94%) | ||||
| 4/470 (0.9%) | 1,3/470 (3%) | 4/470 (0.9%) | 6/471 (1%) | ||||
| 621 bits (780) | 583 bits (732) | 617 bits (776) | 637 bits (800) | ||||
| WOB2pgp12 | 10,727–11,203 | – | – | 30,774–31,244 | 27,485–27,942 | 10,825–11,295 | 828,029–828,499 |
| 439/477 (92%) | 423/464 (91%) | 439/477 (92%)* | 436/477 (91%) | ||||
| 6/477 (1%) | 6/464 (1%) | 6/477 (1%) | 6/477 (1%) | ||||
| 603 bits (758) | 570 bits (716) | 603 bits (758)* | 591 bits (742) | ||||
| WOB2pgp13 | 11,220–11,689 | – | – | 31,261–31,457 | 27,966–28,160 | 11,312–11,508 | 828,51,6–828,712 |
| 192/197 (97%) | 181/195 (93%) | 197/197 (100%) | 188/197 (95%) | ||||
| 0/197 (0%) | 0/195 (0%) | 0/197 (0%) | 0/197 (0%) | ||||
| 294 bits (368) | 256 bits (320) | 31,4 bits (394) | 278 bits (348) | ||||
| 31,523–31,808 | 28,238–28,509 | 11,574–11,859 | 828,790–828,858 | ||||
| 267/288 (93%) | 243/273 (89%) | 246/287 (86%) | 66/69 (96%) | ||||
| 6/288 (2%) | 3/273 (1%) | 4/287 (1%) | 0/69 (0%) | ||||
| 370 bits (464) | 313 bits (392) | 299 bits (374) | 99.1 bits (122) | ||||
| 1–354 | 32,392–32760 | 29,086–29,454 | 13,027–13,386 | – | |||
| 341/369 (92%) | 339/369 (92%) | 334/360 (93%) | |||||
| 15/369 (4%) | 15/369 (4%) | 6/360 (2%) | |||||
| 464 bits (582) | 456 bits (572) | 465 bits (584) | |||||
| WOB2pgp14 | – | 348–21,78 | – | 32,754–34,575 | 29,448–31,278 | 13,380–15,200 | – |
| 1,653/1,832 (90%) | 1,664/1,840 (90%) | 1,679/1,831 (92%) | |||||
| 19/1,832 (1%) | 18/1,840 (1%) | 22/1,831 (1%) | |||||
| 21,84 bits (2,750) | 2,209 bits (2,782) | 2,287 bits (2,880) | |||||
| WOB2pgp15 | – | 2,176–2,400 | – | 34,576–34,800 | 31,276–31,500 | 15,212–15,430 | – |
| 172/225 (76%) | 224/225 (99%)* | 194/219 (89%) | |||||
| 0/225 (0%) | 0/225 (0%) | 0/219 (0%) | |||||
| 167 bits (184) | 401 bits (444)* | 282 bits (312) | |||||
| WOB2pgp16 | – | 2,401–3,785 | – | 34,801–36,228 | 31,501–32,928 | 16,129–16,829 | – |
| Phage portal protein | 1,215/1,439 (84%) | 1,228/1,440 (85%)* | 584/713 (82%) | ||||
| 65/1,439 (5%) | 67/1,440 (5%) | 15/713 (2%) | |||||
| 1,344 bits (1,692) | 1,392 bits (1,752)* | 610 bits (766) | |||||
| – | – | 16,880–17,508 | |||||
| 540/650 (83%) | |||||||
| 25/650 (4%) | |||||||
| 576 bits (724) | |||||||
| WOB2pgp17 | – | 3,818–4,888 | – | 36,255–37,331 | 32,955–33,967 | 17,551–18,566 | – |
| Putative minor capsid protein | 985/1,077 (91%)* | 907/1,024 (89%) | 809/1,030 (79%) | ||||
| 6/1,077 (1%) | 12/1,024 (1%) | 21/1,030 (2%) | |||||
| 1,528 bits (1,694)* | 1,312 bits (1,454) | 830 bits (920) | |||||
| WOB2pgp18 | – | 4,863–5,231 | – | 37,306–37,667 | 34,030–34,391 | 18,629–18,996 | – |
| 331/362 (91%)* | 299/367 (81%) | 323/368 (88%) | |||||
| 3/362 (1%) | 13/367 (4%) | 0/368 (0%) | |||||
| 451 bits (566)* | 303 bits (380) | 406 bits (51,0) | |||||
| WOB2pgp19 | – | 5,273–6,280 | – | 37,715–38,715 | 34,430–35,429 | 19,031–20,015 | – |
| 928/1,002 (93%)* | 918/1,001 (92%) | 910/986 (92%) | |||||
| 1/1,002 (0.1%) | 1/1,001 (0.1%) | 1/986 (0.1%) | |||||
| 1,297 bits (1632)* | 1,260 bits (1586) | 1,263 bits (1590) | |||||
| WOB2pgp20 | – | 7,485–7,805 | – | 38,807–39,1,26 | 35,51,4–35,833 | 20,1,29–20,193 | – |
| 298/320 (93%) | 295/320 (92%) | 53/65 (82%) | |||||
| 0/320 (0%) | 0/320 (0%) | 0/65 (0%) | |||||
| 422 bits (530) | 410 bits (51,4) | 57.8 bits (70) | |||||
| WOB2pgp21 | – | 7,798–8,285 | – | 39,1,20–39,608 | 35,827–36,306 | 20,496–20,915 | – |
| 467/489 (96%) | 458/489 (94%) | 300/422 (71%) | |||||
| 1/489 (0.2%) | 1,0/489 (2%) | 37/422 (9%) | |||||
| 689 bits (866) | 646 bits (812) | 157 bits (196) | |||||
| WOB2pgp22 | – | 8,266–8,698 | – | 39,589–40,021 | 36,287–36,761 | 20,952–21,359 | – |
| 430/433 (99%) | 419/478 (88%) | 351/409 (86%) | |||||
| 0/433 (0%) | 6/478 (1%) | 2/409 (0.5%) | |||||
| 676 bits (850) | 521 bits (654) | 419 bits (526) | |||||
| WOB2pgp23 | – | 8,726–9,054 | – | – | – | – | – |
| WOB2pgp25 | – | – | 316–651 | 40,773–41,08 | 37,871–38,206 | – | – |
| 326/336 (97%) | 328/336 (98%) | ||||||
| 0/336 (0%) | 0/336 (0%) | ||||||
| 562 bits (622) | 571 bits (632) | ||||||
| WOB2pgp26 | – | – | 661–1,470 | 4,118–41,894 | 38,21,6–39,001 | 22,471–23,245 | – |
| 739/789 (94%) | 747/798 (94%) | 535/799 (67%) | |||||
| 1,2/789 (2%) | 12/798 (2%) | 24/799 (3%) | |||||
| 1,204 bits (1,334) | 1,216 bits (1,348) | 250 bits (276) | |||||
| WOB2pgp27 | – | – | – | 41,922–42,083 | 39,020–39,181 | 23,439–24,361 | – |
| 136/162 (84%) | 136/162 (84%) | 672/933 (72%) | |||||
| 0/162 (0%) | 0/162 (0%) | 20/933 (2%) | |||||
| 176 bits (194) | 176 bits (194) | 484 bits (536) | |||||
| 42,132–43,139 | 39,230–40,237 | – | |||||
| 980/1,008 (97%) | 978/1,008 (97%) | ||||||
| 0/1,008 (0%) | 0/1,008 (0%) | ||||||
| 1,692 bits (1876) | 1,683 bits (1866) | ||||||
| WOB2pgp28 | – | – | 2,794–3,476 | 43,160–43,844 | 40,258–40,939 | – | – |
| 61,7/685 (90%) | 543/688 (79%) | ||||||
| 4/685 (1%) | 13/688 (2%) | ||||||
| 816 bits (1,026) | 508 bits (638) | ||||||
| WOB2pgp29 | – | – | 3,492–5,414 | 43,863–45,796 | 40,958–42,910 | – | – |
| 1,769/1,935 (91%) | 1,742/1,953 (89%) | ||||||
| 14/1,935 (1%) | 30/1.953 (2%) | ||||||
| 2,403 bits (3,026) | 2,239 bits (2,820) | ||||||
| WOB2pgp30 | – | – | 5,427–6,610 | 45,822–46,996 | 42,922–44,108 | – | – |
| 1,076/1,175 (92%) | 1,082/1,187 (91%) | ||||||
| 1/1,175 (0.1%) | 4/1,187 (0.3%) | ||||||
| 1,473 bits (1,854) | 1,465 bits (1,844) | ||||||
| WOB2pgp31 | – | – | 6,615–6,811 | 47,001–47,195 | 44,124–44,310 | – | – |
| 157/197 (80%) | 145/191 (76%) | ||||||
| 2/197 (1%) | 6/191 (3%) | ||||||
| 154 bits (192) | 118 bits (146) | ||||||
| WOB2pgp32 | – | – | 6,808–8,298 | 47,192–47,518 | 44,330–44,651 | – | – |
| 302/327 (92%) | 279/322 (87%) | ||||||
| 0/327 (0%) | 0/322 (0%) | ||||||
| 477 bits (528) | 387 bits (428) | ||||||
| 47,607–48,612 | 44,740–45,719 | ||||||
| 926/1,018 (91%) | 909/992 (92%) | ||||||
| 12/1,018 (1%) | 12/992 (1%) | ||||||
| 1,424 bits (1578) | 1,416 bits (1,570) | ||||||
| WOB2pgp33 | – | – | 8,304–8,594 | 48,626–48,910 | 45,760–46,051 | – | – |
| 225/286 (79%) | 239/292 (82%) | ||||||
| 3/286 (1%) | 1/292 (0.3%) | ||||||
| 211 bits (264) | 254 bits (318) | ||||||
| WOB2pgp42 | – | – | 8,593–9,193 | 55,791–56,398 | 51,536–52,143 | – | – |
| 581/608 (96%) | 581/608 (96%) | ||||||
| 7/608 (1%) | 7/608 (1%) | ||||||
| 976 bits (1082) | 976 bits (1,082) | ||||||
| WOB2pgp43 | – | – | 9,121–9,692 | 56,319–56,900 | 52,064–52,645 | – | – |
| 488/590 (83%) | 488/590 (83%) | ||||||
| 26/590 (4%) | 26/590 (4%) | ||||||
| 513 bits (644) | 513 bits (644) | ||||||
| WOB2pgp44 | – | – | 9,831–10,049 | 57,025–57,243 | 52,770–52,988 | – | – |
| 216/219 (99%) | 21,0/219 (96%) | ||||||
| 0/219 (0%) | 0/219 (0%) | ||||||
| 337 bits (422) | 313 bits (392) | ||||||
| WOB2pgp45 | – | – | 10,023–10,922 | 57,217–58,116 | 52,962–53,866 | – | – |
| 858/902 (95%) | 848/905 (94%) | ||||||
| 4/902 (0.4%) | 5/905 (0.6%) | ||||||
| 1,255 bits (1,580) | 1,208 bits (1,520) | ||||||
| WOB3pgp45 | – | – | 11,124–11,696 | – | 54,016–54,588 | – | – |
| SpvB insect toxin | 475/573 (83%) | ||||||
| 0/573 (0%) | |||||||
| 522 bits (656) |
†
Predicted gene products are named and numbered in the “gene name” column; homology-based predicted functional information is also provided. Gene names are based on their homology to gene products reported for the WO reference genome WOcauB2 (Kent et al., 2011a). WOcauB2 paralogs gene product is abbreviated as “WOB2pgp” followed by an identifying number; WOB2pgp13 is thus a paralogs sequence of WOcauB2 gene product 13.
§
NCBI accession numbers of the three contigs generated in this study are provided directly below their names: sr1WOdamA1 contig 1 to 3.
‡
GenBank accession numbers, gene co-ordinates and similarity values for all four of the other sr1WO phage genomes (for a schematic overview of shared sr1WO group genomic architecture see Figure 2). Divergence measurements from WOdamA1 predicted products are displayed for all the paralogs gene sequences that occur in these other four sr1WO genomes. Quoted sequence co-ordinates and similarity values were obtained from individual gene product BLASTn sequence searches of GenBank's non-redundant nucleotide sequence deposits using sr1WOdamA1 predicted gene products as queries and implementing the following search parameters: word size 7; gap opening penalty 0; extension penalty 4. Similarity values are displayed only if they were recovered from the top 10 most significant sequence matches (based on bit scores) found from GenBank's entire non-redundant sequence repository.
*
Bold type face highlights BLASTn sequence similarity matches that were the most significant sequence matches found in all of GenBank's entire non-redundant sequence repository.