Table 4. Wolbachia genome assemblies.
Information on Wolbachia draft genome assemblies. Expected host coverage is calculated as (total sequence data/host genome size). “Evidence of multiple infections” indicates whether or not the assembly contains signs pointing to multiple, distinct Wolbachia strains within the same biological host sample used for generating the sequence data (though some of these consisted of pooled individuals). BUSCO comp., BUSCO dup., BUSCO frag., and BUSCO missing refer to the number of BUSCO orthologs that were found to be complete and single copy, duplicated, fragmented, and missing from the Wolbachia assembly, out of 148 BUSCOs present in the Bacteria odb9 reference gene set. Grey rows at the bottom of the table were omitted from the whole-genome phylogenetic analysis because the assemblies appeared less complete (as indicated by missing BUSCO genes) or showed evidence of being chimeric or a mixture of two independent strains.
| Host species/ID | Description/ common name | BioSample accession number | SRA accession numbers | Total seq. data (Gb) | Host genome size (ref.) | Expected host coverage (x) | Wolbachia median cov. (x) | Wolbachia assembly size (Mbp) | Wolbachia assembly N50 (kb) | BUSCO comp. | BUSCO dup. | BUSCO frag. | BUSCO missing | Evidence of multiple infections? | Sample notes |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| Anopheles gambiae | Mosquito | SAMEA3911293 |
ERR1554906
ERR1554870 ERR1554834 |
9.1 | 280 Mb Holt (2002) | 32 | 9.0 | 1.212 | 23.12 | 125 | 0 | 2 | 21 | No | |
| Biorhiza pallida 1 | Wasp | SAMEA2053316 | ERR233308 | 8.7 | 16 | 1.249 | 9.5 | 125 | 0 | 5 | 18 | No | |||
| Biorhiza pallida 2 | Wasp | SAMEA2053315 | ERR233309 | 8.3 | 16 | 1.246 | 10.29 | 128 | 0 | 3 | 17 | No | |||
| Delias oraia | Butterfly | SAMN05712507 | SRR4341246 | 13.2 | 26 | 1.207 | 13.35 | 124 | 0 | 4 | 20 | No | Wild caught whole insect | ||
| Diabrotica virgifera virgifera 1 | Western corn rootworm | SAMN02373824 |
SRR1106898
SRR1106897 SRR1106544 |
98.9 | 2.4 Gb (GCA_003013835.1) | 41 | 900 | 1.505 | 31 | 128 | 0 | 3 | 17 | No | 5 animals |
| Diabrotica virgifera virgifera 2 | Western corn rootworm | SAMN02373827 |
SRR1106912
SRR1106546 |
95.1 | 2.4 Gb (GCA_003013835.1) | 40 | 750 | 1.487 | 35.01 | 128 | 0 | 3 | 17 | No | 5 animals |
| Diabrotica virgifera virgifera 3 | Western corn rootworm | SAMN02373842 |
SRR1107707
SRR1107708 SRR1107710 SRR1107712 |
88.9 | 2.4 Gb (GCA_003013835.1) | 37 | 660 | 1.376 | 32.16 | 128 | 0 | 3 | 17 | No | 5 animals |
| Diachasma alloeum | Wasp | SAMN03701895 |
SRR2042503
SRR2046752 |
56.8 | 390 Mb (GCA_001412515.1) | 150 | 830 | 1.377 | 21.39 | 127 | 1 | 2 | 18 | No | Adults collected from Rhagoletis pupae, so there may be some contamination with Rhagoletis DNA |
| Diaphorina citri 1 | Asian citrus psyllid | SAMN00100712 |
SRR189238
SRR183690 |
25 | 490 Mb (GCA_000475195.1) | 51 | 180 | 1.379 | 25.7 | 128 | 0 | 2 | 18 | No | |
| Diaphorina citri 2 | Asian citrus psyllid | SAMN01886038 |
SRR649417
SRR649429 SRR649431 SRR649432 SRR649434 |
27.1 | 490 Mb (GCA_000475195.1) | 55 | 250 | 1.425 | 25.7 | 128 | 0 | 2 | 18 | No | |
| Diploeciton nevermanni | Beetle | SAMN05860871 | SRR4342174 | 24.8 | 63 | 1.698 | 10.59 | 124 | 0 | 5 | 19 | No | |||
| Diplolepis spinosa 1 | Gall wasp | SAMEA3930570 | ERR1359308 | 6.8 | 57 | 1.398 | 12.93 | 127 | 0 | 3 | 18 | No | |||
| Diplolepis spinosa 2 | Gall wasp | SAMEA3930574 | ERR1359312 | 7.1 | 53 | 1.382 | 12.13 | 121 | 0 | 3 | 24 | No | |||
| Drosophila melanogaster 1 | Fruit fly | SAMEA3634594 |
ERR1092813
ERR1092814 ERR1092815 ERR1092816 ERR1092817 ERR1092818 |
18.1 | ∼175 Mb | 100 | 1600 | 1.208 | 19.19 | 127 | 0 | 3 | 18 | No | FM7a-23229-hemizygous |
| Drosophila melanogaster 2 | Fruit fly | SAMN04017483 | SRR2347338 | 3.5 | ∼175 Mb | 20 | 21 | 1.198 | 13.83 | 125 | 0 | 4 | 19 | No | Haploid embryos; natural population |
| Drosophila simulans 1 | Fruit fly | SAMEA4395362 | ERR1597896 | 25.3 | ∼150 Mb | 170 | 390 | 1.265 | 14.67 | 130 | 0 | 2 | 16 | No | |
| Drosophila simulans 2 | Fruit fly | SAMEA4394322 | ERR1597899 | 23.4 | ∼150 Mb | 160 | 1100 | 1.294 | 15.57 | 130 | 0 | 2 | 16 | No | |
| Drosophila simulans 3 | Fruit fly | SAMEA4394323 | ERR1597900 | 37 | ∼150 Mb | 250 | 1600 | 1.313 | 15.72 | 130 | 0 | 2 | 16 | No | |
| Drosophila triauraria 1 | Fruit fly | SAMD00051863 | DRR061000 | 22.6 | ∼170 for other Drosophila | 130 | 150 | 1.306 | 22.94 | 129 | 0 | 3 | 16 | No | Female |
| Drosophila yakuba 1 | Fruit fly | SAMN04044077 | SRR2318687 | 8 | ∼170 Mb | 47 | 42 | 1.254 | 14.75 | 128 | 0 | 2 | 18 | No | Pooled isofemale lines (11 lines, 4 females per line) |
| Drosophila yakuba 2 | Fruit fly | SAMN04044078 | SRR2318706 | 4.4 | ∼170 Mb | 26 | 35 | 1.26 | 10.24 | 127 | 0 | 2 | 19 | No | Pooled isofemale lines (11 lines, 4 females per line) |
| Ecitophya simulans | Rove beetle | SAMN05833357 | SRR4301374 | 22.7 | 170 | 1.437 | 42.92 | 127 | 1 | 3 | 17 | No | Whole insect | ||
| Gerris buenoi 1 | Water striders | SAMN02439785 | SRR1197265 | 27.4 | 990 Mb (GCA_001010745.2) | 28 | 69 | 1.538 | 13.14 | 127 | 0 | 3 | 18 | No | Female, whole individuals, adults |
| Gerris buenoi 2 | Water striders | SAMN02439786 | SRR1197267 | 27.8 | 990 Mb (GCA_001010745.2) | 28 | 39 | 1.537 | 13.14 | 127 | 0 | 3 | 18 | No | Male, whole individuals, adults |
| Homalodisca vitripennis 1 | Glassy-winged sharpshooter (leafhopper) | SAMN02209956 |
SRR941995
SRR941996 SRR941997 |
107.7 | 1.45 Gb (GCA_000696855.2) | 74 | 260 | 1.675 | 14.19 | 121 | 9 | 3 | 15 | Maybe: BUSCO duplications | Lab reared Florida-strain female |
| Maconellicoccus hirsutus | Mealybug | SAMEA3699093 | ERR1189167 | 9.8 | 160 Mb (GCA_900064465.1) | 61 | 80 | 1.415 | 27.94 | 130 | 0 | 2 | 16 | No | |
| Operophtera brumata | Winter moth | SAMN03121611 |
SRR1618545
SRR1618581 SRR1618582 |
22.2 | 640 Mb (GCA_001266575.1) | 35 | 28 | 1.35 | 33.34 | 129 | 0 | 1 | 18 | No | Female; adult; head and thorax; wild caught individual |
| Pararge aegeria | Speckled wood butterfly | SAMN02688782 | SRR1190479 | 9.8 | 138 | 1.282 | 83.56 | 129 | 0 | 2 | 17 | No | Whole adult, lab culture | ||
| Pediaspis aceris 1 | Gall wasp | SAMEA3925672 | ERR1355090 | 3.8 | 12 | 1.188 | 8.62 | 119 | 0 | 5 | 24 | No | |||
| Pediaspis aceris 2 | Gall wasp | SAMEA3925673 | ERR1355091 | 3.8 | 12 | 1.174 | 8.05 | 114 | 0 | 9 | 25 | No | |||
| Polygonia c-album | Comma butterfly | SAMN02688783 | SRR1190476 | 6 | 61 | 1.463 | 22.09 | 129 | 0 | 1 | 18 | No | Whole adult, lab cultured | ||
| Pseudomyrmex sp. PSW-54 | Ant | SAMN03275520 | SRR1742977 | 36.9 | 280 Mb (GCA_002006095.1 for congeners) | 130 | 195 | 1.245 | 15.91 | 127 | 0 | 3 | 18 | No | Adult female worker ant |
| Rhagoletis pomonella | Apple maggot fly | SAMN05388941 |
SRR3900841
SRR3901027 |
23.3 | 0.97 (C-value) | 25 | 270 | 1.314 | 13.52 | 127 | 0 | 3 | 18 | No | Single adult female fly |
| Trichogramma pretiosum | Wasp | SAMN02439301 |
SRR1191749
SRR1191750 SRR1191751 SRR1191752 SRR1191753 |
68.6 | 190 Mb (GCA_000599845.3) | 360 | 50 | 1.097 | 51.37 | 127 | 0 | 3 | 18 | No | |
| Acromyrmex echinatior | Ant | SAMEA762107 |
ERR034187
ERR03416 |
13.2 | 300 Mb (GCA_000204515.1) | 44 | 56 | 1.611 | 4.66 | 104 | 0 | 8 | 36 | No | 1 male |
| Bembidion lapponicum | Beetle | SAMN04276907 | SRR2939026 | 8.5 | 11 | 1.151 | 1.79 | 70 | 0 | 13 | 65 | No | Adult, whole body | ||
| Biorhiza pallida 3 | Wasp | SAMEA2053314 | ERR233313 | 4.1 | 4.2 | 0.645 | 0.7 | 3 | 0 | 8 | 137 | No | |||
| Callosobruchus chinensis | Bean weevil | SAMN02313283 |
SRR949786
SRR952345 |
32.1 | 0.75 (C-value) | 44 | 340 | 2.894 | 4.06 | 78 | 6 | 12 | 52 | Yes: bimodal coverage distribution; assembly size; BUSCO duplications | Male, head, thorax, feet |
| Ceratina calcarata | Carpenter bee | SAMN04210145 | SRR2912519 | 16 | 200 Mb (GCA_001652005.1) | 80 | 11 | 1.053 | 1.96 | 55 | 0 | 12 | 81 | No | 1 haploid male |
| Cynipini 1 | Oak gall wasp | SAMEA1965365 |
ERR233303
ERR233304 ERR233305 |
9.4 | 20 | 1.216 | 6.57 | 96 | 0 | 13 | 39 | No | |||
| Cynipini 2 | Oak gall wasp | SAMEA2053318 | ERR233306 | 7.3 | 17 | 1.182 | 3.32 | 82 | 0 | 21 | 45 | No | |||
| Dactylopius coccus | Domestic cochineal | SAMN02725055 |
SRR1231828
SRR1231831 SRR1231832 |
6.2 | 21.1 Mb (estimate given in from NCBI BioSample entry) | 290 | 110 | 2.563 | 5.95 | 47 | 80 | 2 | 19 | Yes: assembly size; BUSCO duplications; bimodal coverage distribution | Bulk sample of 50 Oaxacan Mexican grana |
| Drosophila melanogaster 3 | Fruit fly | SAMN05417645 | SRR3931592 | 3.4 | ∼175 Mb | 19 | 6.5 | 1.171 | 6.14 | 102 | 0 | 15 | 31 | No | Adult male whole body, wild caught from Africa |
| Homalodisca vitripennis 2 | Glassy-winged sharpshooter (leafhopper) | SAMN02209957 | SRR941998 | 39.5 | 1.45 Gb (GCA_000696855.2) | 27 | 64 | 1.803 | 17.02 | 109 | 23 | 3 | 13 | Maybe; BUSCO duplications | Lab-reared Florida-strain male |
| Isocolus centaureae 1 | Gall wasp | SAMEA3930555 | ERR1359249 | 3.4 | 7.9 | 0.998 | 2.19 | 63 | 0 | 16 | 69 | No | |||
| Isocolus centaureae 2 | Gall wasp | SAMEA3930556 | ERR1359250 | 3.4 | 7.7 | 0.965 | 2.31 | 63 | 0 | 14 | 71 | No | |||
| Megacopta cribraria | Stink bug | SAMN02313994 | SRR1145746 | 5.7 | 31 | 2.097 | 1.74 | 75 | 4 | 13 | 56 | Yes: assembly size; BUSCO duplications; possible bimodal coverage distribution | |||
| Mycopsylla fici 1 | Fig psyllid | SAMN04226368 | SRR2954433 | 0.9 | 9.9 | 1.171 | 2.32 | 76 | 0 | 6 | 66 | No | |||
| Mycopsylla fici 2 | Fig psyllid | SAMN04226369 | SRR2954467 | 0.8 | 12 | 1.238 | 2.68 | 77 | 0 | 14 | 57 | No | |||
| Mycopsylla proxima | Psyllid | SAMN04226370 | SRR2954473 | 1.1 | 5.7 | 0.364 | 0.76 | 0 | 0 | 3 | 145 | No | |||
| Rhagoletis zephyria | Tephritid fly | SAMN04977950 |
SRR3670118
SRR3670117 SRR3670120 |
132.9 | 1.1 Gb (GCA_001687245.1) | 120 | 1200 | 1.881 | 11.19 | 80 | 51 | 2 | 15 | Yes: bimodal coverage distribution; assembly size; BUSCO duplications | Single adult female fly |