Table 1.

Summary of reference genomes used for mapping

Organism name	Sequence ID	Accession	Reference
Acyrthosiphon pisum	Genome	SAMN00000061	[85]
Buchnera aphidicola	Genome APS	BA000003.2	[86]
	Plasmid pLeu	AP001071.1	[86]
	Plasmid pTrp	AP001070.1	[86]
Hamiltonella defensa 5AT	Genome 5AT	CP001277.1	[87]
	Plasmid pHD5AT	CP001278.1	[87]
	Phage APSE1	AF157835.1	[88]
	Phage APSE3	EU794053.1	[46]
	Phage APSE4	EU794051.1	[46]
	Phage APSE5	EU794050.1	[46]
	Phage APSE6	EU794054.1	[46]
	Phage APSE7	EU794052.1	[46]
Regiella insecticola 5.15	Genome	AGCA01000000	[89]
	Plasmid pRILSR1	CM000957.1	[90]
Serratia symbiotica strain Tucson	Genome	GCA_000186485.2	[91]
Spiroplasma sp.	Genome	Upon request	[42]
Fukatsuia symbiotica	Genome	GCA_900128755.1	[44]
Rickettsiella viridis	Genome	AP018005.1	[92]
Rickettsia sp.	Genome	Upon request	This paper
	plasmid pREIS3	CM000771.1
	plasmid pRF	GQ329881.1
	plasmid pRAF	CP001613.1
Wolbachia sp. wRi	Genome	GCA_000022285.1	[93]