Variant Surface Glycoprotein gene repertoires in Trypanosoma brucei have diverged to become strain-specific

BMC Genomics

Table 2 Comparison of VSG N-terminal domains of field VSGs with genomic VSG sequences

database name	Tbb gene with greatest identity	NTD ORF intact?	identity (%)	Tbg gene with greatest identity	NTD ORF intact?	identity (%)	difference in % identities
VSG Ako 1	contig 11608	No	73	gamb276c12.p1k_3	Yes	84	11
VSG Ako 2	Tb11.24.0011	Yes	79	gamb843f08.p1k	No	79	0
VSG Bug 1	Tb927.5.190	Yes	58	gamb1660g03.q1k H	Yes	50	8
VSG Bug 2	-	-	-	gamb856d03.q1k_1	Yes	93
VSG Buteba 1	Tb10.v04.0152	Yes	69	gamb333c09.p1k H	partial	67	2
VSG Buteba 2	-	-	-	gamb1441g08.p1k H	partial	84
VSG Buteba 3	Tb09.142.0130	No	84	gamb1420g06.q1k H	Yes	92	8
VSG Buteba 4	Tb927.3.390	No	67	chr3	No	74	7
VSG Buteba 6	Tb927_11_02_v4	Yes	46	-	-	-
VSG Buw 1	Tb09.244.0090	No	80	gamb217f04.p1k	No	69	11
VSG Buw 2	Tb05.26C7.320	No	74	-	-	-
VSG Do 1	Tb09.244.1110	Yes	45	gamb261a02.p1k	Yes	44	1
VSG Do 2	tryp_XI-346e09.p1k	No	64	-	-	-
VSG Kinu 1	Tb09.244.0250	Yes	95	gamb606g06.q1k H	-	93	2
VSG Maw-ero 1	-	-	-	gamb1327e07.q1k	partial	42
VSG Mul 1	-	-	-	-	-	-
VSG Mul 3	Tb10.v4.0093	No	83	gamb86e09.p1k H	No	85	2
VSG Mul 4	Tb09.244.1190	Yes	80	gamb248h03.p1k H	No	72	8
Average			71			73

The N-terminal domains of the VSGs expressed by field isolates have similar percentage identities to homologues from T. b. brucei as to homologues from T. b. gambiense. The 'NTD ORF intact?' column indicates whether the genomic homologue encoded an N-terminal domain that was apparently functional and the percentage identity is over the whole N-terminal domain or all the available sequence (see Supplementary Material).

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