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

BMC Genomics

Table 1 Comparison of VSGs from field isolates with VSG sequences present in the genome of T. brucei brucei TREU927 and T. brucei gambiense Dal972

Tororo VSG	ssp.	domains	Tbb 927 VSG with greatest identity	genomic VSG intact?	genomic sequence complete?	endpoint(s) of identity within ORF?	Tbg Dal VSG with greatest identity	genomic VSG intact?	genomic sequence complete?	endpoint(s) of identity within ORF?	Tororo VSG accession number
VSG Ako 1	Tbr	B1	contig 11608	No	partial	?	gamb276c12.p1k_3	No	Yes	CTD	AJ937323
VSG Ako 2	Tbb	B1	Tb11.24.0011	No	Yes	CTD	gamb843f08.p1k	No	Yes	CTD	AJ937324
VSG Bug 1	Tbb	A3	Tb927.5.190	No	Yes	SS CTD	gamb1660g03.q1k H	No	Yes	SS CTD	AJ560648
VSG Bug 2	Tbb	B2	-	-	-	-	gamb856d03.q1k_1	No	Yes	CTD	AJ937318
VSG Buteba 1	Tbb	B2	Tb10.v04.0152	No	Yes	CTD	gamb333c09.p1k H	-	partial	?	AJ549081
VSG Buteba 2	Tbb	A2	-	-	-	-	gamb1441g08.p1k H	No	partial	?	AJ937312
VSG Buteba 3	Tbb	B1	Tb09.142.0130	No	Yes	CTD	gamb1420g06.q1k H	No	Yes	CTD	AJ937316
VSG Buteba 4	Tbb	A2	Tb927.3.390	No	Yes	CTD	chr3	No	Yes	CTD	AJ937321
VSG Buteba 6	Tbb	B1	Tb927_11_02_v4	No	Yes	CTD	-	-	-	-	AJ937329
VSG Buw 1	Tbb	B2	Tb09.244.0090	No	Yes	CTD	gamb217f04.p1k	No	Yes	SS CTD	AJ937326
VSG Buw 2	Tbr	A2	Tb05.26C7.320	No	Yes	CTD	-	-	-	-	AJ937328
VSG Do 1	Tbr	B2	Tb09.244.1110	No	Yes	SS hinge	gamb261a02.p1k	No	Yes	SS hinge	AJ937315
VSG Do 2	Tbr	B1	tryp_XI-346e09.p1k	No	partial	?	-	-	-	-	AJ937325
VSG Kinu 1	Tbb	A2	Tb09.244.0250	Yes	Yes	outside ORF	gamb606g06.q1k H	-	partial	?	AJ937313
VSG Maw-ero 1	Tbr	B1	-	-	-	-	gamb1327e07.q1k	No	Yes	SS	AJ937314
VSG Mul 1	Tbr	B2	-	-	-	-	-	-	-	-	AJ937317
VSG Mul 3	Tbb	B2	Tb10.v4.0093	No	Yes	CTD	gamb86e09.p1k H	No	partial	?	AJ937320
VSG Mul 4	Tbb	B2	Tb09.244.1190	No	Yes	CTD	gamb248h03.p1k H	No	Yes	CTD	AJ937327

Most of the VSGs expressed by field isolates are present in the genome sequences of both T. brucei brucei TREU927 and T. brucei gambiense Dal972. The table shows the name of the VSG from the Tororo district, whether it is from T. b. brucei (Tbb) or T. b. rhodesiense (Tbr) and the domain type combination. The most similar VSG in the genome sequences of T. b. brucei TREU927 and T. b. gambiense Dal972 is then given, the cut off for inclusion was sequence identity of > 40 % over the whole of the VSG. In some cases the sequence was from manual assembly of individual sequencing runs into contigs and these are available in the Supplementary Material and are marked H after the identifier. The 'intact VSG' column indicates whether the VSG sequences in the genome encode a potentially functional VSG ORF (Berriman et al. 2005). The 'database entry complete' column indicates whether the sequence contig or sequence read spanned the entire potential ORF. The endpoints of identity column indicates where, within the VSG amino acid sequence, the high percentage identity ended: SS, N-terminal signal sequence; hinge, linker between the two domains; CTD, C-terminal domain.

ISSN: 1471-2164