Supplementary materials

Lateral transfers of insertion sequences between Wolbachia, Cardinium and Rickettsiabacterial endosymbionts

Olivier Duron

1

Bacterial strains / Host species (Class: Order: Family) / Method of ISRpe1 detection (reference) / ISRpe1 distribution / GenBank accession number
ISRpe1 / 16S rRNA(*) or wsp (**)
BACTEROIDETES
Cardinium hertigii
cPlu strain / Holocnemus pluchei (Arachnida: Araneae: Pholcidae) / specific PCR assays (this study) / present / KC677596, KC677597 and KC677598 / EU333930 *
unnamed strain / Phalangium opilio (Arachnida: Opilones: Phalangiidae) / specific PCR assays (this study) / _ / _ / KC677578 *
unnamed strain / Ixodes scapularis (Arachnida: Ixodida: Ixodidae) / specific PCR assays(Felsheim et al., 2009) / present / GU166817 / AB001518 *
unnamed strain / Dermanyssus gallinae (Arachnida: Acari: Dermanyssidae) / specific PCR assays (this study) / _ / _ / KC677579 *
unnamed strain / Tetranychus urticae (Arachnida: Acari: Tetranychidae) / specific PCR assays (this study) / present / KC677599 / KC677580 *
unnamed strain / Unidentified honey bee mite (Arachnida: Acari) / specific PCR assays (this study) / present / KC677600 / KC677581 *
unnamed strain / Encarsia hispida (Insecta: Hymenoptera: Aphelinidae) / specific PCR assays (this study) / present / KC677601 / KC677582 *
cEper1 strain / Encarsia pergandiella (Insecta: Hymenoptera: Aphelinidae) / whole genome sequencing (Penz et al., 2012) / present / NC018605 and NC018606 / NC018605 *
unnamed strain / Scaphoideus titanus (Insecta: Hemiptera: Cicadellidae) / specific PCR assays (this study) / present / KC677602 / KC677583 *
unnamed strain / Bemesia tabacci (Insecta: Hemiptera: Aleyrodidae) / specific PCR assays (this study) / _ / _ / KC677584 *
unnamed strain / Aspidiotus nerii (Insecta: Hemiptera: Diaspididae) / specific PCR assays (this study) / _ / _ / KC677585 *
Amoebophilus asiaticus
5a2 strain / Acanthamoeba spp. (Amoebozoa: Euamoebida: Acanthamoebidae) / whole genome sequencing (Schmitz-Esser et al., 2010) / present / NC010830 / NC010830 *
EIDS3 strain / Acanthamoeba spp. (Amoebozoa: Euamoebida: Acanthamoebidae) / specific PCR assays (Schmitz-Esser et al., 2011) / present / HM159373 / AM408794 *
ALPHAPROTEOBACTERIA
Wolbachia pipientis
unnamed strain / Pholcus phalangioides (Arachnida: Araneae: Pholcidae) / specific PCR assays (this study) / present / KC677603 / EU333938 *
unnamed strain / Guignotus pusillus (Insecta: Coleoptera: Dytiscidae) / specific PCR assays (this study) / present / KC677604 / EU727133 *
unnamed strain / Tribolium confusum (Insecta: Coleoptera: Tenebrionidae) / specific PCR assays (this study) / present / KC677605 / KC677586 *
wRi strain / Drosophila simulans (Insecta: Diptera: Drosophilidae) / whole genome sequencing (Klasson et al., 2009) / present / CP001391 / CP001391 *
wAna strain / Drosophila ananassae (Insecta: Diptera: Drosophilidae) / whole genome sequencing (Salzberg et al., 2005) / present / AAGB01000003, 037, -102, -119, -130, -164, -233, -268, -361, -382, -387 and -436 / AAGB01000004 *
wMel strain / Drosophila melanogaster (Insecta: Diptera: Drosophilidae) / whole genome sequencing (Wu et al., 2004) / present / NC002978 / NC002978 *
wMel strain / Drosophila melanogaster (Insecta: Diptera: Drosophilidae) / specific PCR assays (Cordaux et al., 2008) / present / EU714636 / _
unnamed strain / Drosophila auraria (Insecta: Diptera: Drosophilidae) / specific PCR assays (Cordaux et al., 2008) / present / EU714637 / _
unnamed strain / Drosophila triauraria (Insecta: Diptera: Drosophilidae) / specific PCR assays (Cordaux et al., 2008) / present / EU714638 / _
unnamed strain / Drosophila willistoni (Insecta: Diptera: Drosophilidae) / whole genome sequencing (unpublished) / present / AAQP01000061 and -141 / AAQP01000000 *
unnamed strain / Zaprionus sepsoides (Insecta: Diptera: Drosophilidae) / specific PCR assays (Cordaux et al., 2008) / present / EU714639 / _
wPip(Lv) strain / Culex pipiens pipiens (Insecta: Diptera: Culicidae) / specific PCR assays (this study) / _ / _ / KC677587 *
wPip(Is) strain / Culex pipiens form molestus(Insecta: Diptera: Culicidae) / specific PCR assays (this study) / _ / _ / KC677588 *
wPip(Mol) strain / Culex pipiens form molestus(Insecta: Diptera: Culicidae) / whole genome sequencing (unpublished) / present / CACK01000000 / CACK01000000 *
wPip(Pel) strain / Culex quinquefasciatus (Insecta: Diptera: Culicidae) / whole genome sequencing (Klasson et al., 2008) / present / NC010981 / NC010981 *
wPip(JHB) strain / Culex quinquefasciatus (Insecta: Diptera: Culicidae) / whole genome sequencing (Salzberg et al., 2009) / present / ABZA00000000 / ABZA00000000 *
wAlbB strain (1) / Aedes albopictus (Insecta: Diptera: Culicidae) / whole genome sequencing (Mavingui et al., 2012) / present / CAGB01000000 / CAGB01000000 *
wAlbB strain (2) / Aedes albopictus (Insecta: Diptera: Culicidae) / specific PCR assays (this study) / present / KC677606 / KC677589*
unnamed strain / Cercopis intermedia (Insecta: Hemiptera: Cercopidae) / specific PCR assays (this study) / present / KC677607 / KC677590*
unnamed strain / Cercopis vulnerata (Insecta: Hemiptera: Cercopidae) / specific PCR assays (this study) / present / KC677608 / KC677591 *
unnamed strain / Cicadella viridis (Insecta: Hemiptera: Cicadellidae) / specific PCR assays (this study) / _ / _ / EU727125 *
unnamed strain / Icerya purchasi (Insecta: Hemiptera: Monophlebidae) / specific PCR assays (this study) / _ / _ / EU727127 *
unnamed strain / Hydrometra stagnorum (Insecta: Hemiptera: Hydrometridae) / specific PCR assays (this study) / _ / _ / EU727126 *
unnamed strain / Notostira elongata (Insecta: Hemiptera: Miridae) / specific PCR assays (this study) / present / KC677609 / EU727130 *
unnamed strain / Sigara lateralis (Insecta: Hemiptera: Corixidae) / specific PCR assays (this study) / _ / _ / EU727136 *
unnamed strain / Cacopsylla pruni (Insecta: Hemiptera: Psyllidae) / specific PCR assays (this study) / present / KC677613 / KC677592 *
unnamed strain / Diplolepis rosae (Insecta: Hymenoptera: Cynipidae) / specific PCR assays (this study) / _ / _ / EU727128 *
unnamed strain / Oomyzus sokolowskii (Insecta: Hymenoptera: Eulophidae) / specific PCR assays (this study) / present / KC677610 / KC677594 **
wLhet1 strain / Leptopilina heterotoma (Insecta: Hymenoptera: Figitidae) / specific PCR assays(Cordaux et al., 2008) / present / EU714635 / _
wUni strain / Muscidifurax uniraptor (Insecta: Hymenoptera: Pteromalidae) / whole genome sequencing (Klasson et al., 2009) / present / ACFP01000210 / _
wVitB strain / Nasonia vitripennis (Insecta: Hymenoptera: Pteromalidae) / whole genome sequencing (Kent et al., 2011) / present / HQ906665 / M84686 *
unnamed strain / Triodia sylvina (Insecta: Lepidoptera: Hepialidae) / specific PCR assays (this study) / _ / _ / EU727124 *
unnamed strain / Gryllus campestris(Insecta: Orthoptera: Gryllidae) / specific PCR assays (this study) / present / KC677611 / KC677595 **
unnamed strain / Gryllomorpha dalmatina (Insecta: Orthoptera: Gryllidae) / specific PCR assays (this study) / present / KC677612 / EU727135 *
wBm strain / Brugia malayi (Chromadorea: Spirurida: Onchocercidae) / whole genome sequencing (Foster et al., 2005) / present / NC006833 / NC006833 *
unnamed strain / Litomosoides sigmodontis (Chromadorea: Spirurida: Onchocercidae) / specific PCR assays (this study) / _ / _ / KC677593 *
unnamed strain / Onchocerca ochengi (Chromadorea: Spirurida: Onchocercidae) / whole genome sequencing (Darby et al., 2012) / present / NC018267 / NC018267 *
Rickettsia spp.
Rickettsia sp. (REIS strain) / Ixodes scapularis (Arachnida: Ixodida: Ixodidae) / whole genome sequencing(Gillespie et al., 2012) / present / ACLC01000041, -067, -092 and -122 / CM000770 *
Rickettsia sp. (MEAM1 strain) / Bemisia tabaci(Insecta: Hemiptera: Aleyrodidae) / whole genome sequencing (Rao et al., 2012) / present / AJWD01000013 / AJWD01000000 *
R. africae (ESF-5 strain) / Amblyomma spp. (Arachnida: Ixodida: Ixodidae) / whole genome sequencing (Fournier et al., 2009) / _ / _ / CP001612 *
R. akari (Hartford strain) / Liponyssoides sanguineus (Arachnida: Acari: Dermanyssidae) / whole genome sequencing (unpublished) / _ / _ / CP003309 *
R. amblyommii (GAT-30V strain) / Amblyomma sp. (Arachnida: Ixodida: Ixodidae) / whole genome sequencing (unpublished) / present / NC017028 / NC017028 *
R. australis (Cutlack strain) / Ixodes spp. (Arachnida: Ixodida: Ixodidae) / whole genome sequencing (unpublished) / _ / _ / CP003338 *
R. australis (Phillips strain) / Ixodes spp. (Arachnida: Ixodida: Ixodidae) / whole genome sequencing (Dong et al., 2012b) / present / AKVZ01000058 / AKVZ00000000 *
R. bellii (OSU85-389 strain) / various tick species (Arachnida: Ixodida: Ixodidae) / whole genome sequencing (unpublished) / present / CP000849 / CP000849 *
R. bellii (RML369-C strain) / various tick species (Arachnida: Ixodida: Ixodidae) / whole genome sequencing (Ogata et al., 2006) / present / CP000087 / CP000087 *
R. canadensis (CA410 strain) / Haemaphysalis leporispalustris (Arachnida: Ixodida: Ixodidae) / whole genome sequencing (unpublished) / present / CP003304 / CP003304 *
R. canadensis (McKiel strain) / Haemaphysalis leporispalustris (Arachnida: Ixodida: Ixodidae) / whole genome sequencing (unpublished) / present / NC009879 / NC009879 *
R. conorii (Malish 7 strain) / Rhipicephalus sanguineus (Arachnida: Ixodida: Ixodidae) / whole genome sequencing (Ogata et al., 2001) / _ / _ / NC003103 *
R. conorii caspia (A-167 strain) / Rhipicephalus sanguineus (Arachnida: Ixodida: Ixodidae) / whole genome sequencing (Sentausa et al., 2012b) / _ / _ / AJUR00000000 *
R. conorii conorii indica (ITTR strain) / Rhipicephalus sanguineus (Arachnida: Ixodida: Ixodidae) / whole genome sequencing (Sentausa et al., 2012c) / _ / _ / AJHC00000000 *
R. conorii israelensis (ISTT CDC1 strain) / Rhipicephalus sanguineus (Arachnida: Ixodida: Ixodidae) / whole genome sequencing (Sentausa et al., 2012d) / _ / _ / AJVP01000000 *
R. felis (URRWXCal2 strain) / Ctenocephalides felis (Insecta: Siphonaptera: Pulicidae) / whole genome sequencing (Ogata et al., 2005) / present / NC007111 and NC007110 / CP000053 *
R. heilongjiangensis (054 strain) / Haemaphysalis concinna (Arachnida: Ixodida: Ixodidae) / whole genome sequencing (Duan et al., 2012) / _ / _ / CP002912 *
R. helvetica (C9P9 strain) / Ixodes spp. (Arachnida: Ixodida: Ixodidae) / whole genome sequencing (Dong et al., 2012a) / present / CM001467 / CM001467 *
R. honei (RB strain) / Bothriocroton hydrosauri (Arachnida: Ixodida: Ixodidae) / whole genome sequencing (Xin et al., 2012) / _ / _ / AJTT00000000 *
R. japonica (YH strain) / Haemaphysalis longicornis (Arachnida: Ixodida: Ixodidae) / whole genome sequencing (unpublished) / _ / _ / AP011533 *
R. massiliae (AZT80 strain) / Rhipicephalus spp. (Arachnida: Ixodida: Ixodidae) / whole genome sequencing (unpublished) / _ / _ / NC016931 *
R. massiliae (MTU5 strain) / Rhipicephalus spp. (Arachnida: Ixodida: Ixodidae) / whole genome sequencing (Blanc et al., 2007) / present / NC009900 / NC009900 *
R. montanensis (OSU 85-930 strain) / Dermacentor spp. (Arachnida: Ixodida: Ixodidae) / whole genome sequencing (unpublished) / _ / _ / CP003340 *
R. parkeri (Portsmouth strain) / Amblyomma maculatum (Arachnida: Ixodida: Ixodidae) / whole genome sequencing (unpublished) / _ / _ / CP003341 *
R. peacockii (DaE100R strain) / Dermacentor andersoni (Arachnida: Ixodida: Ixodidae) / specific PCR assays(Simser et al., 2005) / present / AY996135 / _
R. peacockii (Rustic strain) / Dermacentor andersoni (Arachnida: Ixodida: Ixodidae) / whole genome sequencing (Felsheim et al., 2009) / present / NC012730 and NC012732 / NC012730 *
R. philipii (364D strain) / Dermacentor occidentalis (Arachnida: Ixodida: Ixodidae) / whole genome sequencing (unpublished) / _ / _ / CP003308 *
R. prowazekii (BuV67-CWPP strain) / Pediculus humanus humanus (Insecta: Phthiraptera: Pediculidae) / whole genome sequencing (unpublished) / _ / _ / CP003393 *
R. prowazekii (Chernikova strain) / Pediculus humanus humanus (Insecta: Phthiraptera: Pediculidae) / whole genome sequencing (unpublished) / _ / _ / CP003391 *
R. prowazekii (Dachau strain) / Pediculus humanus humanus (Insecta: Phthiraptera: Pediculidae) / whole genome sequencing (unpublished) / _ / _ / CP003394 *
R. prowazekii (GvV257 strain) / Pediculus humanus humanus (Insecta: Phthiraptera: Pediculidae) / whole genome sequencing (unpublished) / _ / _ / CP003395 *
R. prowazekii (Katsinyian strain) / Pediculus humanus humanus (Insecta: Phthiraptera: Pediculidae) / whole genome sequencing (unpublished) / _ / _ / CP003392 *
R. prowazekii (Madrid E strain) / Pediculus humanus humanus (Insecta: Phthiraptera: Pediculidae) / whole genome sequencing (Andersson et al., 1998) / _ / _ / AJ235269 *
R. prowazekii (Rp22 strain) / Pediculus humanus humanus (Insecta: Phthiraptera: Pediculidae) / whole genome sequencing (unpublished) / _ / _ / CP001584 *
R. prowazekii (RpGvF24 strain) / Pediculus humanus humanus (Insecta: Phthiraptera: Pediculidae) / whole genome sequencing (unpublished) / _ / _ / CP003396 *
R. rickettsii (Arizona strain) / various tick species (Arachnida: Ixodida: Ixodidae) / whole genome sequencing (unpublished) / _ / _ / CP003307 *
R. rickettsii (Brazil strain) / various tick species (Arachnida: Ixodida: Ixodidae) / whole genome sequencing (unpublished) / _ / _ / CP003305 *
R. rickettsii (Colombia strain) / various tick species (Arachnida: Ixodida: Ixodidae) / whole genome sequencing (unpublished) / _ / _ / CP003306 *
R. rickettsii (Hauke strain) / various tick species (Arachnida: Ixodida: Ixodidae) / whole genome sequencing (unpublished) / _ / _ / CP003318 *
R. rickettsii (Hino strain) / various tick species (Arachnida: Ixodida: Ixodidae) / whole genome sequencing (unpublished) / _ / _ / CP003309 *
R. rickettsii(Hlp#2 strain) / various tick species (Arachnida: Ixodida: Ixodidae) / whole genome sequencing (unpublished) / _ / _ / CP003311 *
R. rickettsii (Iowa strain) / Dermacentor variabilis (Arachnida: Ixodida: Ixodidae) / whole genome sequencing (unpublished) / _ / _ / CP000766 *
R. rickettsii (Sheila Smith strain) / various tick species (Arachnida: Ixodida: Ixodidae) / whole genome sequencing (unpublished) / _ / _ / CP000848 *
1 / R. rhipicephali (3-7-female6-CWPP strain) / Rhipicephalus sanguineus (Arachnida: Ixodida: Ixodidae) / whole genome sequencing (unpublished) / present / NC017042 / NC017042 *
R. sibirica (246 strain) / Dermacentor nuttali (Arachnida: Ixodida: Ixodidae) / whole genome sequencing (unpublished) / _ / _ / AABW01000001 *
R. sibirica mongolitimonae (HA-91 strain) / Hyalomma spp.(Arachnida: Ixodida: Ixodidae) / whole genome sequencing(Sentausa et al., 2012a) / _ / _ / AHZB01000000 *
R. sibirica sibrica (BJ-90 strain) / Dermacentor spp. (Arachnida: Ixodida: Ixodidae) / whole genome sequencing(Sentausa et al., 2012e) / _ / _ / AHIZ01000000 *
R. slovaca (D-CWPP strain) / Dermacentor spp. (Arachnida: Ixodida: Ixodidae) / whole genome sequencing (unpublished) / _ / _ / CP003375 *
R. slovaca (13-B strain) / Dermacentor spp. (Arachnida: Ixodida: Ixodidae) / whole genome sequencing (Fournier et al., 2012) / _ / _ / CP002428 *
R. typhi (B9991CWPP strain) / Fleas (Insecta: Siphonaptera) / whole genome sequencing (unpublished) / _ / _ / CP003398 *
R. typhi (TH1527 strain) / Fleas (Insecta: Siphonaptera) / whole genome sequencing (unpublished) / _ / _ / CP003397 *
R. typhi (Wilmington strain) / Fleas (Insecta: Siphonaptera) / whole genome sequencing (McLeod et al., 2004) / _ / _ / AE017197 *

Table S1.Distribution and sequence accession numbersof ISRpe1 in 102strains of bacterial endosymbionts.Underlined accession numbers represent new sequence data generatedfor this study.

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Bacterial strains / Host species (Class: Order: Family) / ISRpe1 copy / Start position / End position / Length (bp) / Orientation / Structure / Putative IR / Putative Tnp functional status
BACTEROIDETES
Cardinium hertigii
cEper1 strain / Encarsia pergandiella (Insecta: Hymenoptera: Aphelinidae) / copy #1 / 47091 / 48281 / 1191 / + / full length / TGTAGTAGTYARGATWTAMTCTRACA / yes
copy #2 / 87031 / 88221 / 1191 / - / full length / TGTAGTAGTTGRGATWTAMTCTGACA / yes
copy #3 / 183662 / 183710 / 49 / - / 5' and 3' truncated / absent / no
copy #4 / 204584 / 204749 / 166 / + / 5' and 3' truncated / absent / no
copy #5 / 519864 / 521054 / 1191 / + / full length / TGTAGTAGTYAGGATTTAMTCTRAC / yes
copy #6 / 545578 / 546766 / 1189 / - / full length / TGTAGTAGTTRRGATTTAMTCTGACA / yes
copy #7 / 632913 / 634104 / 1192 / + / full length with internal stop codon / TGTAGTAGTYAGGATTTAMTCTRACA / no
copy #8 / 650257 / 651410 / 1154 / - / 5' truncated / TGTCAGAGTAAATCCTGACTACTACA / no
copy #9 / 727118 / 727690 / 573 / + / 5' and 3' truncated / absent / no
copy #10 / 883358 / 883616 / 259 / - / 3' truncated / TGTAGTAGTTGACATTTAATCTTACA / no
copy #11 / 2437 (plasmid) / 2871 (plasmid) / 435 / - / 5' and 3' truncated / absent / no
copy #12 / 5779 (plasmid) / 5904 (plasmid) / 126 / + / 3' truncated / TGTAGTAGTTAGGATTTACTCTGACA / no
Amoebophilus asiaticus
5a2 strain / Acanthamoeba spp. (Amoebozoa: Euamoebida: Acanthamoebidae) / copy #1 / 710151 / 710444 / 294 / - / 5' truncated / TGTACAAGTCAAGATTTAAACTGACA / no
copy #2 / 792262 / 792662 / 401 / - / 5' truncated / TGTACAAGTCAAGATTTAAACTGACA / no
copy #3 / 1119513 / 1120721 / 1209 / - / full length / TGTACWAGTYWAGATTTAAACTGACA / yes
copy #4 / 1198445 / 1199653 / 1209 / - / full length / TGTACWAGTYWAGATTTAAACTGACA / yes
copy #5 / 1238183 / 1239391 / 1209 / - / full length / TGTACWAGTYWAGATTTAAACTGACA / yes
copy #6 / 1587297 / 1587468 / 172 / - / 5' and 3' truncated / absent / no
copy #7 / 1751055 / 1751309 / 255 / + / 5' truncated / TGTACAAGTCAAGATTTAAACTGACA / no
ALPHAPROTEOBACTERIA
Wolbachia pipientis
wRi strain / Drosophila simulans (Insecta: Diptera: Drosophilidae) / copy #1 / 69257 / 70445 / 1189 / - / full length / TGTAWWARAYAAGAYTTGAYTCTGACA / yes
copy #2 / 134530 / 134583 / 54 / + / 5' and 3' truncated / absent / no
copy #3 / 176494 / 176550 / 57 / - / 5' and 3' truncated / absent / no
copy #4 / 231163 / 231205 / 43 / - / 5' and 3' truncated / absent / no
copy #5 / 395298 / 396486 / 1189 / - / full length / TGTAWWARAYAAGAYTTGAYTCTGACA / yes
copy #6 / 401380 / 402568 / 1189 / + / full length / TGTAWWARAYAAGAYTTGAYTCTGACA / yes
copy #7 / 402566 / 402968 / 403 / + / disrupted by a 785 bp deletion within Tnp / TGTAWWARAYAAGAYTTGAYTCTGACA / no
copy #8 / 693926 / 695105 / 1180 / + / full length / TGTAWWARAYAAGAYTTGAYTCTGACA / yes
copy #9 / 962558 / 963746 / 1189 / + / full length / TGTAWWARAYAAGAYTTGAYTCTGACA / yes
copy #10 / 978081 / 980551 / 2471 / + / disrupted by an IS (ISWpi1) insertion / TGTAWWARAYAAGAYTTGAYTCTGACA / no
copy #11 / 800169 / 800222 / 54 / - / 5' and 3' truncated / absent / no
wAna strain / Drosophila ananassae (Insecta: Diptera: Drosophilidae) / copy #1 / 11762 (contig gdan400) / 12950 (contig gdan400) / 1180 / - / full length / TGTWARAKAYRAGWWYWRYWCWGACA / yes
copy #2 / 5840 (contig gdan463) / 5972 (contig gdan463) / 134 / - / 5' truncated / TGTCAGATCAAATCTTGTCTTTTACA / no
copy #3 / 5974 (contig gdan463) / 6238 (contig gdan463) / 265 / + / 3' truncated / TGTATTAAATAAGACTTGACCTGACA / no
copy #4 / 6239 (contig gdan463) / 7427 (contig gdan463) / 1180 / - / full length / TGTWARAKAYRAGWWYWRYWCWGACA / yes
copy #5 / 883 (contig gdan410) / 1665 (contig gdan410) / 783 / - / 5' and 3' truncated / absent / no
copy #6 / 1 (contig gdan138) / 767 (contig gdan138) / 767 / + / 5' truncated? (end of contig) / TGTCAGATCAAATCTTGTCTTTTACA / unknown