Table 1. Orthologs identified in gene content analysis as lost or gained at nodes A-D.

For some regions of difference (RD), the first and/or last gene in the region was not identified in our analysis because enough of the gene remained to align to H37Rv, and thus was not considered absent. Gene names starting with an O were identified through our SYNERGY orthogroup analysis. Nodes A-D were identified in Fig 2.

A: root node of lineage 6				C: root node of lineage 5
	loss	Annotation	RD		loss	Annotation	RD
	Rv0124	PE-PGRS family protein PE_PGRS2	RD701		Rv1334	hydrolase	RD711
B: root node of lineage 6 and M. bovis					Rv1335	sulfur carrier protein CysO	RD711
	loss	Annotation	RD		Rv1523	methyltransferase
	Rv0222	enoyl-CoA hydratase EchA1	RD10		Rv1978	hypothetical protein	RD713
	Rv1965	ABC transporter permease YrbE3B	RD7		Rv1979c	permease	RD713
	Rv1966	MCE-family protein Mce3A	RD7		Rv1993c	hypothetical protein	RD743
	Rv1967	MCE-family protein Mce3B	RD7		Rv1994c	ArsR family transcriptional regulator CmtR	RD743
	Rv1968	MCE-family protein Mce3C	RD7		Rv1995	hypothetical protein	RD743
	Rv1969	MCE-family protein Mce3D	RD7		Rv3514	PE-PGRS family protein PE_PGRS57
	Rv1970	MCE-family lipoprotein LprM	RD7	D: root node of lineages 5 and 6 and M. bovis
	Rv1971	MCE-family protein Mce3F	RD7		loss	Annotation	RD
	Rv1972	MCE-associated membrane protein	RD7		Rv2073c	oxidoreductase	RD9
	Rv1973	MCE-associated membrane protein	RD7		Rv2074	pyridoxamine 5'-phosphate oxidase	RD9
	Rv1974	membrane protein	RD7		Rv2084	hypothetical protein
	Rv1975	hypothetical protein	RD7
	Rv1976c	hypothetical protein	RD7		gained	Annotation	RD
	Rv3617	epoxide hydrolase EphA	RD8		O850451604	PPE family protein
	Rv3618	monooxygenase	RD8
	Rv3619c	ESAT-6 like protein EsxV	RD8
	Rv3620c	ESAT-6 like protein EsxW	RD8
	Rv3621c	PPE family protein PPE65	RD8
	Rv3622c	PE family protein PE32	RD8
	gained	Annotation	RD
	O850447630	hypothetical protein
	O850450572	PE-PGRS family protein