Table 4.

Pathotype-specific putative pseudogenes, genic frameshifts and truncations

Pathotype	Gene	Description	Native coordinates	Alignment coordinates	Gene fragment 1	Gene fragment 2	Note
A		methyltransferase domain	60851-61836	61748-62734	XANAC_0061	XAC0050	Putative ψ
	LacZ	beta-galactosidase	838208-841101	850951-853845	XAC0707	XAC0708	Putative ψ
		putative secreted protein	986002-986826	999771-1000595	XAC0825	XANAC_0965	Putative ψ
	oppD/yliA	ABC transporter	1021079-1022728	1034920-1036570	XAC0859	XAC0860	Putative ψ
	araJ	MFS transporter	3326112-3327329	3414846-3416063	XAC2837	XAC2836	Putative ψ
	rarD	Permease – chloramphenicol resistence	4693056-4693966	4830382-4831292	XAC4000	XAC4001	Putative ψ
	catB	catalase	4719198-4720710	4856716-4858239	XAC4029	XAC4030	Putative ψ
A*		PbsX Transcription Factor	614013-614472	630726-631530	XAC71A_130207	XAC71A_130208	Putative ψ
		acyl-CoA synthetase	1041072-1042552	1063009-1064489	XAC71A_170122	XAC71A_170123	Putative ψ
			1622056-1625651	1640494-1644089	XAC71A_280103	XAC71A_280104	Putative ψ
			1860274-1860803	1904352-1904881	XAC71A_310052	XAC71A_310053	Putative ψ
	rpfB	acyl-CoA synthetase	2187629-2189311	2300143-2301825	XAC71A_390075	XAC71A_390076	Putative ψ
			2269033-2269866	2382037-2382870	XAC71A_410007	XAC71A_410008	Putative ψ
		GGDEF family protein	2286218-2289170	2399383-2402335	XAC71A_410020	XAC71A_410021	Putative ψ
	comA	competence protein	2447016-2449565	2572127-2574695	XAC71A_450029	XAC71A_450030	Putative ψ
	XACSR11	carboxypeptidase	3101427-3102721	3299904-3301198	XAC71A_660002	XAC71A_660003	Putative ψ
	xopN	type III effector	3293500-3295557	3508783-3510840	XAC71A_730134		Putative ψ, truncated 3′
	yagT	putative oxidoreductase, 2Fe-2S subunit	3420879-3421529	3641125-3641775	XAC71A_740038	XAC71A_740039	Putative ψ
	yodB	Cytochrome B561	3563369-3564046	3785148-3785825	XAC71A_750009		frameshift, longer 3′
	xopL	type III effector	3641485-3643372	3864216-3866109	XAC71A_760048	XAC71A_760049	Putative ψ
	rimK	Ribosomal protein S6 modification protein	3847131-3848050	4111446-4112365	XAC71A_840004	XAC71A_840005	Putative ψ
			3998076-3997795	4263201-4262920	XAC71A_880069		Putative ψ, truncated 5′
Aw			59860-61116	60605-61861	XAC3218_20024	XAC3218_20025	Putative ψ
	adh	alcohol dehydrogenase	247107-247385	256015-256293	XAC3218_100056		Putative ψ, truncated 3′
	yojM	superoxide dismutase-like	256565-257695	265546-267635	XAC3218_110001	XAC3218_110002	Putative ψ
			3010085-3008397	3123577-3121889	XAC3218_630012		longer
		LysR Transcription Factor	4453733-4452393	4671211-4669871	XAC3218_910186		longer
		exported	4957802-4960197	5228371-5230773	XAC3218_960285	XAC3218_960286	Putative ψ
			4962702-4964291	5233406-5234995	XAC3218_970002	XAC3218_970003	Putative ψ
	ttcA	2-thiocytidine biosynthesis protein TtcA	4988408-4989507	5261994-5263093	XAC3218_990014	XAC3218_990015	Putative ψ
	xylB	xylulose B	5015663-5013780	5290774-5288891	XAC3218_990034		longer