Patterns of gene recombination shape var gene repertoires in Plasmodium falciparum: comparisons of geographically diverse isolates

Kraemer, Susan M; Kyes, Sue A; Aggarwal, Gautam; Springer, Amy L; Nelson, Siri O; Christodoulou, Zoe; Smith, Leia M; Wang, Wendy; Levin, Emily; Newbold, Christopher I; Myler, Peter J; Smith, Joseph D

doi:10.1186/1471-2164-8-45

Table 2 High scoring BLASTn matches within and between isolates.

From: Patterns of gene recombination shape var gene repertoires in Plasmodium falciparum: comparisons of geographically diverse isolates

Comparison isolates	var1	var2	Chromosome/group var1	Chromosome/group var2	% ID	Match length (nt)
between
HB3x3D7	HB3var2	MAL8P1.207 ^a	7/A1ST	8/A1ST	93.62	1175
HB3x3D7	HB3var2	PFD1235w ^a	7/A1ST	4/A1ST	93.62	1175
HB3x3D7	HB3var4	PF13_0003	A1ST	13/A1ST	91.19	636
HB3x3D7	HB3var22	PF11_0521	8/B1C	11/A1ST	92.62	664
HB3x3D7	HB3var23	PFL1950w	12/B4C^b	12/B4C	99.59	972
ITxHB3	IT4var28	HB3var35	UpsC2	7/C1C	99.34	1057
ITxHB3	ITvar16	HB3var37(inc)	UpsB2	UpsB1	97	661
ITxHB3	FCR3S1.2_1	HB3var27	unknown	B3C	99	1703
3D7xIT	PFD0020c	IT4var6	4/A1ST	unknown	90	536
within
3D7x3D7^c	PFD0635w	PFD0630c	4/B3C	4/C1C	99	703
3D7x3D7	PFD0635w	PFD0630c	4/B3C	4/C1C	99.78	3645
3D7x3D7	PFD1000c	PFD0995c	4/C1C	4/C1C	100	2831
3D7x3D7	PFD1005c	PFD1000c	4/B1C	4/C1C	99.92	2551
3D7x3D7	MAL13P1.1	PFE0005w	13/B1T	5/B1T	100	2776
HB3xHB3	HB3var3	HB3var4	11/A1ST	A1ST	100	4948
HB3xHB3	HB3var23	HB3var24	12/B3C	8/B4C	94.52	1240
HB3xHB3	HB3var23	HB3var24	12/B3C	8/B4C	93.12	567
HB3xHB3	HB3var26	HB3var23	12/B3C	12/B3C	96.56	552
HB3xHB3	HB3var25	HB3var24	8/B3C	8/B4C	92.86	518
HB3xHB3	HB3var15(inc)	HB3var14	B1T	10/B1T	100	788
HB3xHB3	HB3var15(inc)	HB3var14	B1T	10/B1T	99.76	1657
HB3xHB3	HB3var20	HB3var14	B1T	10/B1T	100	2577
HB3xHB3	HB3var7	HB3var8	B1ST	B1T	99.86	5016
ITxIT	CS2	IT4_var7	6/unknown	UpsA1	99.67	905
ITxIT	IT4var41	IT4_var16	UpsB1	12/UpsB2	97.58	2359
ITxIT	CS2	IT4_var19	6/unknown	UpsB1	99.28	2221
ITxIT	CS2	IT4_var29	6/unknown	1/UpsB1	99.63	804
ITxIT	CS2	IT4_var29	6/unknown	1/UpsB1	93.69	697
ITxIT	CS2	A4varICAM	6/unknown	13/B1T	100	777
ITxIT	FCR3S1.2_1	IT4var58	4/unknown	unknown	98	1046
ITxIT	IT4var23	IT4var58	unknown	unknown	99	615
ITxIT	IT4var6	IT4var19	unknown	UpsB1	92	1348

^aMAL8P1.207 and PFD1235w are duplicated in 3D7, so the match with HB3var2 effectively occurs only once.
^bThese two genes have a unique UpsB4 type 5' flanking sequence and are the first genes in a chromosome 12 central cluster in HB3 and 3D7, respectively.
^cHighlighted rows indicate multiple hits of high sequence similarity, shared between the same gene pairs.

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ISSN: 1471-2164

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