Complexity of the MSG gene family of Pneumocystis carinii

BMC Genomics

Table 1 Frequencies of putative MSG alleles in five populations of P. carinii

Group^a (no. reads)	Nucleotide position of polymorphism^b	Haplotypes^c	Frequency of haplotypes in 5 P. carinii populations^d
			A	B	C	D	E
1(49)	HV1, 81	1-C	15	3	1	1	5
		1-T	0	2	0	0	0
		2-C	4	15	0	0	1
		2-T	0	1	0	0	0
		3-C	1	0	0	0	0
		4-C	1	0	0	0	0
2 (40)	57,83,173,204	5-GTAA	6	24	0	0	0
		5-TTAA	0	2	0	0	0
		5-GCAA	0	2	0	0	0
		5-GTGA	4	0	0	0	0
		5-GTAT	2	0	0	0	0
3 (34)	HV1, 85, 203	4-CT	9	16	1	0	1
		4-CG	1	0	1	0	0
		6-CT	0	0	0	0	1
		6-CG	2	0	0	0	0
		5-GG	1	0	1	0	0
4 (32)	HV1	7	10	16	1	0	0
		8	2	0	0	0	0
		9	0	0	1	1	0
		10	1	0	0	0	0
5 (29)	153	11-T	5	22	0	0	0
		11-C	0	2	0	0	0
6 (28)	HV1, 300	12-T	4	20	1	0	0
		12-C	0	2	0	0	0
		13-T	1	0	0	0	0
7 (26)	193	14-A	2	22	0	0	0
		14-G	0	2	0	0	0
8 (24)	HV1	9	13	7	0	0	1
		7	2	0	0	1	1
9 (25)	HV1,302,313	4-AA	3	14	0	0	0
		4-GA	0	4	0	0	0
		4-AG	0	2	0	0	0
		1-AA	1	0	0	0	0
		15-AA	1	0	0	0	0
10 (19)	97 to 107	16	8	10	0	0	0
		16-indel	1	0	0	0	0
12 (18)	65,216,228,282	18-T-TA	2	11	0	0	0
		18-A-TA	0	1	0	0	0
		18-AATG	0	1	0	0	0
		18-TATA	0	1	0	0	0
		18-T-AA	0	2	0	0	0
13 (16)	HV1	9	1	0	0	0	0
		16	15	0	0	0	0

^a 581 reads were assembled (maximum mismatch of 5%) into groups. Groups containing less than 16 reads are not listed.
^b "HV1" means that a polymorphism was seen in hypervariable region 1 (see Table 2 for sequences). Numbers in this column refer to the location of the polymorphisms that were not in HV1. Each number refers to a nucleotide site where position 1 is the A in the ATG at the beginning of the CRJE. Because the HV1 sequences varied in length, the position-numbers of polymorphisms downstream of HV1 cannot be compared between groups.
^c An haplotype designated as 1-C had a type 1 hypervariable region and a C at a polymorphic site located outside of HV1.
^d Populations A and B were the source of ADAM plasmids and Lucigen genome project reads, respectively. Populations C, D and E were smaller populations that had been analyzed in the past using the same methods as those used to produce the ADAM plasmid library.

ISSN: 1471-2164