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Table 1 Orthologs of WSSV genes identified on the three viral scaffolds of Metopaulias depressus

From: Characterization of fossilized relatives of the White Spot Syndrome Virus in genomes of decapod crustaceans

Scaffold Position, bp Strand Length, bp Predicted protein length, aa ORF number in WSSV b Protein in WSSV   Truncated ends Frameshifts g MAFFT alignment
      CN TH TW Family c Protein length Function d     Pairwise identity, % Alignment length, aa
I 2,517-3,356 - 840 279 299 147 355   309      21.1 341
I 3,524-5,980 + 2,457 818 303 149 359   891 TATA box binding protein (TBP)     48.3 894
I 8,084-12,361 - 4,278 1,425 151 89 207   1,436 Latency-related     26.8 1,538
I 13,933-17,373 + 3,441 1,145 11 36 67   1,301 VP53A, VP150 E 3’   41.2 1,326
I 19,141-21,198 + 2,058 685 220 112 275   674 VP674, VP76, class I cytokine receptor C    37.6 703
I 22,400-24,835 - 2,436 811 172 92 228   848 Ribonucleotide reductase large subunit (RR1)     55.4 850
I 24,958-28,317 + 3,360 1,119 166 91 222 (NA) 1,072      35.0 1,166
I 29,688-35,294 + 5,607 1,868 447 9 507   1,936 Helicase     43.5 1,986
I 36,408-43,088 + 6,681 2,227 a 143 84 198   2,314     Poly 22.9 2,509
I 43,108-44,328 + 1,221 406 188 98 243   413 Ribonucleotide reductase small subunit (RR2)     47.3 442
I 45,135-45,998 + 864 288 (112) (71) (168)   462 dUTPase     22.8 468
I 46,200-47,384 - 1,185 394 446 7 + 8 506   526      19.4 563
I 47,874-52,274 + 4,401 1,466 465 16 524   1,243 VP136B     19.3 1,546
I 52,821-55,352 - 2,532 843 45 43 102   981      35.1 1,020
I 55,376-58,807 - 3,432 1,143 37 42 94   1,279 VP160B C    49.2 1,309
I 59,002-61,614 + 2,613 870 119 73 175   1,044      32.8 1,084
I 61,759-62,034 + 276 91 35 41 92   972 VP110 E 5’, fragment e   50.0 i 973 i
II 898-18,972 - 18,075 6,024 360 167 419   6,077 VP664 C    50.6 6,221
II 19,204-31,302 + 12,099 4,031 343 165 + 166 399 + 412   4,180      38.0 4,331
II 31,716-34,289 + 2,574 857 423 2 482   730 Protein kinase 1 (PK1)     35.0 888
II 34,316-34,906 - 591 196 421 1 480   204 VP28 E    25.5 204
II 35,421-38,787 + 3,367 1,120 a 139 82 194   1,208     STR 39.8 1,247
II 38,756-39,691 + 936 311 137 81 192   337 VP337     25.4 351
II 40,142-41,488 - 1,347 448 a 131 77 186   484     Poly 33.4 495
II 41,511-42,371 + 861 286 133 78 188   271      33.4 302
III 561-848 - 288 95 21 37 77   200 hr-binding protein   5’; 3’ e   15.7 204
III 927-1,754 - 828 275 23 38 79   286      37.2 289
III 1,820-2,215 - 396 131 25 39 81   231    5’ e   16.2 247
III 2,231-6,865 - 4,635 1,543 26 40 86 + 82   1,535 VP507     50.2 1,590
III 8,195-11,185 - 2,991 996 226 114 281   936      27.2 1,074
III 11,727-14,753 - 3,027 1,008 192 100 247   1,019      44.8 1,051
III 14,831-15,739 + 909 302 191 99 246   311 Endonuclease     44.9 325
III 17,211-18,929 - 1,719 572 427 3 486   623 Latency-related     34.2 658
III 19,167-22,964 + 3,798 1,265 433 4 492 + 496   1,261      51.6 1,323
III 23,005-24,687 + 1,683 560 440 5 500   607      46.2 623
III 24,642-27,239 + 2,598 865 442 6 502   800 VP800, VP95 T    30.4 895
III 30,327-33,310 - 2,984 994 a 64 + 63 53 121 + 120   843     Poly 16.4 1,099
III 38,213-40,172 - 1,960 653 277 135 332   791      31.6 807
III 40,595-44,461 - 3,867 1,289 271 134 326   1,219 VP136A C   Poly 36.1 1,348
III 44,426-44,971 + 546 181 270 133 325   170      34.2 190
III 44,938-46,377 + 1440 479 269 132 324   489 VP53c     53.9 505
III 46,469-47,209 + 741 246 267 131 321   281      28.1 281
III 47,325-49,637 + 2,313 770 260 130 315   922 VP387     25.3 965
III 50,920-52,581 - 1,662 553 1 30 52   1,684 VP1684, collagen E    23.5 i 613 i
III 52,725-55,115 - 2,391 796 332 160 388   786 VP75     38.2 824
III 55,224-57,680 + 2,457 818 327 159 383   856 VP90 E    40.1 872
III 58,441-59,865 + 1,425 473 147 85 202   459      19.8 515
III 62,523-63,143 - 621 206 419 (NA) 478   193      31.9 210
III 62,963-64,516 - 1,554 517 415 183 474   544 VP544, VP60 § C    43.0 547
III 64,652-65,005 + 354 117 414 182 473   121 VP19 E    39.3 122
III 65,332-65,604 + 273 90 324 157 380   82      31.3 98
III 65,906-66,142 - 237 78 322 156 378   227    5’, 3’; fragment   16.1 i 227 i
III 66,363-66,752 - 390 129 321 155 377   117 VP13B, VP16 E    39.5 129
III 66,908-69,883 + 2,976 991 313 154 369   1,179      29.9 1,224
III 69,974-70,567 + 594 197 311 153 367   204 VP26 T    28.2 206
III 70,645-71,418 - 774 257 310 152 366   272      33.0 277
III 71,415-72,818 - 1,404 467 308 151 364   466 VP466, VP51 C    44.4 480
III 72,809-73,111 - 303 100 306 150 362   419 VP39A T 5’ e   10.8 435
III 73,422-75,302 + 1,881 626 282 140 337   634      54.1 658
III 75,443-77,426 + 1,984 660 a 161 90 217   759     Poly 29.8 786
III 77,503-84,399 + 6,897 2,298 514 27 39   2,351 DNA polymerase     55.0 2,409
III 84,915-86,372 + 1,458 485 no homology    Inhibitor of apoptosis protein      
III 86,662-87,348 - 687 228 295 146 351   209      23.6 267
III 87,428-87,922 - 495 164 294 145 350   206      17.6 216
III 88,010-88,258 + 249 82 293a 144 349   97 VP14   5’ ef   55.3 97
III 88,215-92,825 + 4,611 1,536 289 143 344   1,564 VP160A, VP190 C    38.1 1,627
III 93,236-96,400 - 3,165 1,054 285 142 340   1,100      36.9 1,116
III 96,852-98,046 - 1,195 398 a 78 59 135   398 hr-binding protein    Poly 20.9 460
  1. abased on protein sequences after “correction” of the frameshifts
  2. bAccession numbers for the three reference genomes see in text. ORF identification numbers are taken either from original publications or from GenBank annotations. Cases of frameshifts in the WSSV genomes are marked with “+” connecting two parts of the original ORF. “(NA)” marks an ORF present in WSSV-TH genome, but not annotated
  3. cfamilies of paralogs according to [8]. “(NA)” marks one family not reported in that study
  4. dbased largely on the summary presented by [1]. Structural proteins are prefixed with “VP”, their location (when known) is marked with letters: C – nucleocapsid; T – tegument; E – envelope
  5. ecases of truncations confirmed with Sanger-sequencing
  6. fadditionally: predicted start codon is non-canonical (ACG)
  7. gcauses of frameshifts (when present, presumably sequencing artefacts): Poly – homopolymer regions; STR – short tandem repeats
  8. hall alignments were performed with the G-INS-i mode. If not noted otherwise, identities are reported for the whole alignments
  9. ibased on truncated alignments