MOESM3 of Global sequence diversity of the lactate dehydrogenase gene in Plasmodium falciparum

Additional file 3. Nucleotide sequence IDs of the ldh gene of the malaria parasites of humans and non-human primates

MOESM4 of Global sequence diversity of the lactate dehydrogenase gene in Plasmodium falciparum

Additional file 4. Neighbour Joining tree of 61 allelic sequences of the gene encoding lactate dehydrogenase (ldh) from 12 Plasmodium parasite species. The sequences are named according to parasite species and allelic type. The first two letters indicate parasite species: Pf (Plasmodium falciparum), Pm (Plasmodium malariae), Po (Plasmodium ovale), Pv (Plasmodium vivax), Pp (Plasmodium praefalciparum), Pr (Plasmodium reichenowi), Pbi (Plasmodium billcollinsi), Pbl (Plasmodium blacklocki), Pa (Plasmodium alderi), Pg (Plasmodium gaboni), Pk (Plasmodium knowlesi) and Pc (Plasmodium cynomolgi). Species showed on the right hand site are labelled with color representing parasite host: Homo sapiens (blue), Gorilla gorilla (black), Pan troglodytes (green) and Macaca fascicularis (red). The tree was constructed using the aligned sequences of 768 nucleotides, corresponding to nucleotide position 52–819 after P. falciparum strain 3D7. Bootstrap values are shown next to the nodes. Scale bar shows nucleotide substitution per site

The Comparative Intensities of 92 AFLP markers of <i>Plasmodium chabaudi chabaudi</i> strain AJ from the progeny of a genetic cross between <i>P. c. chabaudi</i> strains CB-pyr10 and AJ following selection in mice immunised strain AJ (see text).

<p>AJ-specific markers (indicated by black diamonds) were located on a <i>P. c. chabaudi</i> genetic linkage map, generated from a genetic cross between AS and AJ <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0000857#pone.0000857-Martinelli2" target="_blank">[34]</a>. Numbers after letter ‘C’ and ‘g’ represent <i>P. c. chabaudi</i> chromosome numbers and <i>P. c. chabaudi</i> unassigned linkage groups, respectively, in the genetic linkage map <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0000857#pone.0000857-Martinelli2" target="_blank">[34]</a>. Of the six AJ markers which were most reduced under AJ-specific immune selection (see <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0000857#pone-0000857-t002" target="_blank">Table 2</a>), five (indicated by asterisks) could be located to <i>P. c. chabaudi</i> chromosome 8, forming a selection valley with the <i>P. c. chabaudi msp</i>-1 gene at its lowest point (see text). RTQ-PCR values for the proportions of the AJ-immune selected cross progeny carrying the AJ alleles of the Merozoite Surface Protein-1 (<i>msp</i>-1) are indicated by the red triangle and Apical Membrane Antigen-1 (<i>ama</i>-1) by the green triangle in the AJ-immune selected cross progeny. The red line indicates Comparative Intensity of 50%.</p

Physical and genetic locations of AFLP markers of <i>Plasmodium chabaudi chabaudi</i> strain AJ whose Comparative Intensities (CI) were reduced below 50% in the progeny of the genetic cross between CB-pyr10 and AJ following selection in an AJ-immunised mouse (see text).

<p>The six AJ markers with CI of <20% in the AJ-immune selected cross progeny mapped to positions closely linked to the gene encoding the <i>P. c. chabaudi</i> merozoite surface protein-1 (MSP-1) are indicated in bold. ND not determined.</p>*<p>The first and second numbers in brackets represent percentages of parasite DNA carrying the AJ alleles of the indicated gene ( <i>msp</i>-1 or <i>ama</i>-1), respectively in the AJ-immune selected cross progeny and in the non-immune selected cross progeny, as measured by RTQ-PCR (see text)</p>**<p>Numbers after ‘<i>pf</i>’’ indicate the <i>Plasmodium falciparum</i> chromosome number followed by distance along the chromosome in kilo base pairs</p

The parameters used to calculate the predicted maximum number of recombinant lines present in the pooled progeny of the genetic cross between strains CB-pyr10 and AJ of <i>Plasmodium chabaudi chabaudi</i>.

<p>The predicted number of such recombinants is calculated as described (see <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0000857#s4" target="_blank"><i>Materials and Methods</i></a>). SEM, standard error of mean.</p

Course of blood stage induced infection of the uncloned CB x AJ cross progeny grown in a non-immune mouse (dotted line with open circles), in a CB-immunised mouse (pink line filled squares) and in an AJ-immunised mouse (blue line with filled symbols).

<p>Arrows indicate day of infection when the uncloned cross progeny grown in the immunised mice or the non-immune mouse were sub-inoculated for expansion in non-immune mice (see text).</p

Additional file 1: Figure S1. of Size and sequence polymorphisms in the glutamate-rich protein gene of the human malaria parasite Plasmodium falciparum in Thailand

Map showing the sampling site locations for Plasmodium falciparum collection in Thailand. Abbreviations: MH, Mae Hong Son; K, Kanchanaburi, RN, Ranong; UB, Ubon Ratchatani; TD, Trat. (DOC 67 kb

Additional file 5: Table S4. of Size and sequence polymorphisms in the glutamate-rich protein gene of the human malaria parasite Plasmodium falciparum in Thailand

Distribution of the GLURP subtypes in 65 P. falciparum isolates in Thailand. Bold letters indicate the 10 GLURP subtypes that are prevalent in more than one endemic site in Thailand (DOC 92 kb

Additional file 4: Table S3. of Size and sequence polymorphisms in the glutamate-rich protein gene of the human malaria parasite Plasmodium falciparum in Thailand

The percentage of the aspartic acid (D) and glutamic acid (E) insertions at the end of Block 4 to 15 sequences in R2 region of P. falciparum GLURP gene. (DOC 34 kb

MOESM3 of Genetic diversity of the merozoite surface protein-3 gene in Plasmodium falciparum populations in Thailand

Additional file 3. Variants of the MSP-3 protein sequence in reference strains of Plasmodium falciparum