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Page 4 of 16 Stuehler et al. Microbiome Res Rep. 2025;4:19 https://dx.doi.org/10.20517/mrr.2024.84

Table 1. List of all Wolbachia strains and accessions used in phylogenetic analysis
Taxonomy (order: GenBank
Host name Common name Strain Supergroup Abbreviation
family) accession
Anastrepha South American fruit Diptera: Tephritidae clone 46.1 A wAfra† KC589027.1
fraterculus fly
Carposina sasakii Peach fruit moth Lepidoptera: wCauA A wCsas NZ_CP041215.1
Carposinidae
Ceratosolen solmsi Fig wasp Hymenoptera: MIAOwCsol A wCsol CP054598.1
Agaonidae
Drosophila ananassae Fruit fly Diptera: Drosophilidae wAna A wDana CP042904.1
Drosophila incompta Fruit fly Diptera: Drosophilidae wInc Cu A wDinc NZ_CP011148.1
Drosophila Fruit fly Diptera: Drosophilidae wMelpop A wDmel CP046921.1
melanogaster
Drosophila simulans Fruit fly Diptera: Drosophilidae wAu A wDsim1 CP069055.1
Hypothenemus Coffee berry borer Coleoptera: H control 1 A wHham† KX436087.1
hampei Curculionidae
Wiebesia pumilae Fig wasp Hymenoptera: MIAOwWpum A wWpum CP054557.1
Agaonidae
Aedes albopictus Tiger mosquito Diptera: Culicidae wAlbB B wAalb CP031221.1
Bactericera cockerelli Potato psyllid Hemiptera: Triozidae clone 3 B wBcoc† KM267307.1
Bemisia tabaci Silverleaf whitefly Hemiptera: Aleyrodidae China 1 B wBtab NZ_CP016430.1
Culex Southern house Diptera: Culicidae wPipPel B wCqui AM999887.1
quinquefasciatus mosquito
Diaphorina citri Asian citrus psyllid Hemiptera: Liviidae dawsonii B wDcit1 CP051608.1
Diaphorina citri Asian citrus psyllid Hemiptera: Liviidae KPSwDI10P38 B wDcit2 CP051265.2
Diaphorina citri Asian citrus psyllid Hemiptera: Liviidae Beihai B wDcit3† GQ385974.1
Diaphorina citri Asian citrus psyllid Hemiptera: Liviidae Shenzhen B wDcit4† GU480072.1
Drosophila mauritiana Fruit fly Diptera: Drosophilidae wMau B wDmau CP034335.1
Drosophila simulans Fruit fly Diptera: Drosophilidae wMa B wDsim2 CP069054.1
Homalodisca Glassy-winged Hemiptera: Cicadellidae GWSS B wHcoa† DQ450164.1
coagulata sharpshooter
Homalodisca elongata Glassy-winged Hemiptera: Cicadellidae B21HE B wHelo† DQ450154.1
sharpshooter
Laodelphax striatellus Small brown Hemiptera: Delphacidae wStri B wLstr NZ_MUIX01000001.1
planthopper
Nilaparvata lugens Brown planthopper Hemiptera: Delphacidae wLug B wNlug NZ_MUIY01000001.1
Spodoptera picta Lily caterpillar Lepidoptera: Noctuidae Spic B B wSpic CP067976.1
Brugia pahangi Filarial nematode Rhabditida: FR3 D wBpah CP050521.1
worm Onchocercidae
Litomosoides Filarial nematode Rhabditida: wLsig D wLsig CP046577.1
sigmodontis worm Onchocercidae
Folsomia candida Springtail Collembola: Isotomidae Berlin E wFcan NZ_CP015510.2
Cimex lectularius Bed bug Hemiptera: Cimicidae wCle F wClec AP013028.1

†: Wolbachia strains included only in the ML phylogenetic tree depicting evolutionary lineage by the wsp gene.

databases using BLASTn. The longest transcripts matching a subject with the lowest E-value scores were
selected for MLST. Phylogenetic analysis was performed using a concatenated form of these conserved
sequences for each of the samples listed in Table 1. As a result of the MLST study, the three most closely
related Wolbachia endosymbionts to wLfag-FL: Spodoptera picta strain Spic_B (CP067976.1), Diaphorina
citri strain dawsonii (CP051608.1), and Laodelphax striatellus strain wStri (NZ_MUIX01000001.1) were
used as reference genomes for HISAT2 v2.0.4 mapping with default parameters to identify Wolbachia
[25]
sequences in the four TRINITY assembled datasets. The resulting sequences were subject to BLASTn
analysis using the NCBI nt database to verify sequence identity across a broader database. If sequences did