Table 1. Wolbachia strains used in comparative and phylogenetic analyses.

Strain	Host	Supergroup	Size (bp)	ORFs	Reference	Accession Number	BUSCO Scorea
wGmm	Glossina morsitans morsitans	A	1,019,687	1378	Brelsfoard et al. (2014)	AWUH00000000	C: 77.5% [D: 6.4%], F: 5%, M: 17.5%, n: 40
wHa	Drosophila simulans	A	1,295,804b	1342	Ellegaard et al. (2013)	CP003884	C: 85% [D: 2.9%], F: 5%, M: 10%, n: 40
wMel	Drosophila melanogaster	A	1,267,782c	1401	Wu et al. (2004)	AE017196	C: 87.5% [D: 2.9%], F: 2.5%, M: 10%, n: 40
wRi	Drosophila simulans	A	1,445,873c	1493	Klasson et al. (2009)	CP001391	C: 82.5% [D: 3%], F: 5%, M: 12.5%, n: 40
wSuzi	Drosophila suzukii	A	1,415,350	1528	Siozios et al. (2013a)	CAOU00000000	C: 87.5% [D: 2.9%], F: 2.5%, M: 10%, n: 40
wAIbB	Aedes albopictus	B	1,162,431	1187	Mavingui et al. (2012)	CAGB00000000	C: 82.5% [D: 3%], F: 2.5%, M: 15%, n: 40
wBol1	Hypolimnas bolina	B	1,377,933	1369	Duplouy et al. (2013)	CAOH00000000	C: 80% [D: 3.1%], F: 5%, M: 15%, n: 40
wDi	Diaphorina citri	B	1,240,904	1250	Saha et al. (2012)	AMZJ00000000	C: 80% [D: 3.1%], F: 2.5%, M: 17.5%, n: 40
wNo	Drosophila simulans	B	1,301,823c	1317	Ellegaard et al. (2013)	CP003883	C: 82.5% [D: 3%], F: 2.5%, M: 15%, n: 40
wPip_Pel	Culex quinquefasciatus Pel	B	1,482,355c	1461	Klasson et al. (2008)	AM999887	C: 80% [D: 3.1%], F: 5%, M: 15%, n: 40
wPip_JBH	Culex quinquefasciatus JBH	B	1,542,137	1556	Salzberg et al. (2009)	ABZA00000000	C: 75% [D: 3.3%], F: 2.5%, M: 22.5%, n: 40
wPip_Mol	Culex pipiens molestus	B	1,340,443c	1340	Pinto et al. (2013)	HG428761	C: 80% [D: 3.1%], F: 2.5%, M: 17.5%, n: 40
wTpre	Trichogramma pretiosum	B	1,133,709b	1405	This study	LKEQ00000000	C: 77.5% [D: 3.2%], F: 5%, M: 17.5%, n: 40
wVitB	Nasonia vitripennis	B	1,107,643	1245	Kent et al. (2011)	AERW00000000	C: 77.5% [D: 3.2%], F: 2.5%, M: 20%, n: 40
wOo	Onchocerca ochengi	C	957,990c	1272	Darby et al. (2012)	HE660029	C: 75% [D: 3.3%], F: 2.5%, M: 22.5%, n: 40
wBm	Brugia malayi	D	1,080,084c	1339	Foster et al. (2005)	AE017321	C: 82.5% [D: 3%], F: 5%, M: 12.5%, n: 40
wWb	Wuchereria bancrofti	D	1,052,327	2144	Desjardins et al. (2013)	ADHD00000000	C: 45% [D: 0%], F: 20%, M: 35%, n: 40
wCle	Cimex lectularius	F	1,250,060c	1357	Nikoh et al. (2014)	AP013028	C: 72.5% [D: 3.4%], F: 2.5%, M: 25%, n: 40

ORFs, open reading frames; BUSCO, benchmarking universal single-copy orthologs; C, complete; D, duplicated; F, fragmented; M, missing; n, number of genes used.

^aBUSCO scores in standard BUSCO notation.

^bSingle-scaffold assembly.

^cComplete assembly.