MOESM1 of Whole genome sequencing of Plasmodium falciparum from dried blood spots using selective whole genome amplification

Additional file 1: Figure S1. A plot of primers (probes) and their binding distribution on the P. falciparum genome. The topmost panel show cumulating binding positions and distribution profile of all the 28 primers. Black dots (1) show positions where the primer binds and Red (0) dots shows positions with no primer binding. Probes are ordered from bottom to top; the first 10 primers is Probe_10, followed by Probe_20 then Probe_28. Figure S2. Coverage depths frequencies of samples with different parasitaemia levels. Figure S3. Coverage of genes associated with drug resistance. Colours reflect the percentage of genome covered, ranging from 5x (grey) to 30x or more (red). Table S1. Non-reference allele frequencies (NRAF) of major drug resistance genes for venous blood (VB; leucodepleted and unamplified) and dried blood spots (DBS; sWGA) samples. Gene name, chromosome number, position, mutation name, mutation type and the NRAF found in West Africa populations (MalariaGen https://www.malariagen.net/apps/pf/4.0/ ) are shown. Notably, the studied populations have high dhfr mutation frequencies and rare crt mutations. Presumably because the use of SP was widespread and is still being used (e.g. pregnancy prophylaxis), whereas enough time has passed since chloroquine was widely used [26–28]. Table S2. Probe_10. sWGA primers for Plasmodium falciparum

Adaptation and performance of rice genotypes in tropical and subtropical environments

Standardized field experiments were carried out to study the performance of five rice genotypes derived from different germplasm in terms of yield, harvest index (HI) and grain quality at eight agro-ecological sites of the tropics and subtropics across Asia during 2001 and 2002. Considering that indica and javanica genotypes adapt to warm climatic conditions, and japonica genotypes to cool agro-climatic conditions, it is hypothesized that indica × japonica hybrids may combine high yields and good quality traits under a wide range of agro-climatic conditions. Grain yield, HI, protein content and amylose content varied considerably among genotypes and environments. Mean rice yields of genotypes ranged from 1.5 to 11 t ha-1 across the eight sites; on average yields were 7.2 t ha-1 under subtropical and 2.7 t ha-1 under tropical conditions. The much lower yields in tropical environments resulted from a low biomass as well as a low HI. Among the genotypes, the indica × japonica hybrid showed the highest yield under subtropical conditions, and a higher yield than the japonica genotypes and the indica × javanica hybrid but lower than the indica genotype under tropical conditions. Phenology of genotypes varied strongly across environments. Low yields at tropical locations were associated with a low light capture due to short growth duration. Post-anthesis light-use efficiencies and the photothermal quotient explained much of the variation in yield. Protein content varied among genotypes depending on location and year. Variation in amylose content of rice grains was mainly associated with genotypic differences and much less with environmental conditions, but contents decreased with higher post-anthesis ambient temperatures. The indica × japonica hybrid combined high yields with a favourable amylose content and showed a better ability to adapt to cool and to warm agro-climatic conditions than the indica or japonica genotypes. Our study showed the magnitude of yield penalties associated with growing rice genotypes in environments to which they are not adapted. The consequences of these findings for improved adaptation of rice are discusse

Correlation coefficients of log2 fold changes (FC) by RT-qPCR and microarray analysis.

<p>The linear regression is indicated on the plot, with an r² = 0.7389.</p

Lumefantrine drug selection regimen.

<p>Number of cycles during which V1S was cultured with varying Lumefantrine (LM) concentrations. In total, parasites were exposed to LM for 166 <i>P. falciparum</i> cycles, finally resulting in LM resistant V1S_LM.</p

Changes in gene expression profiles between LM resistant V1S_LM and LM sensitive V1S <i>P. falciparum</i>.

<p><b>A.</b> Heatmap of 589 expressed genes showing Differential Expression (DE) in at least one time point (F adjusted <i>p</i><0.05). The 2 clusters highlighted with blue and red bars on the right hand side of the heatmap correspond to subtelomeric genes gradually switched off in the presence of LM, and transporters and cell cycle regulators gradually turned on in the presence of LM, respectively. Log2 ratio of V1S_LM vs. V1S expression is indicated by the color key ranging from −6 (blue, under-expression) to 6 (red, over-expression) <b>B.</b> Venn diagram showing the asexual life cycle distribution of DE genes. Analysis was based on linear modeling using Limma package of R/Bioconductor.</p

Chromosomes 2 (A) and 10 (B) show over-expression of contiguous probes covering 21 and 22 CDS, respectively.

<p>Amplification of the signals for the left arms of chromosomes 2 (<b>A</b>) and 10 (<b>B</b>) are enlarged for each time point as indicated. Every single coloured dot corresponds to a 25-mer probe: red is for 0 h, blue for 12 h, green for 24 h and yellow for 36 h. Underneath every enlarged chromosomal arm are pink bars indicating 100% robustness of signal amplification at <i>p</i><0.01 (using SnoopCGH program with Smith–Waterman algorithm implementation). A normal distribution of the log ratios (y-axis) around the zero horizontal line is expected if the expression levels are the same along the chromosome (indicated as kilo base pair [kbp]). The CDS (represented under each chromosome by blue rectangles) contained within each amplified region are indicated on the right with their appropriate annotation (<a href="http://www.genedb.org" target="_blank">www.genedb.org</a>). The genes marked with an * have been found significant at B>0 in the pairwise comparisons of the microarray data in at least one time point, while the underlined genes have been double checked by qRT-PCR.</p

Gene Ontology (GO) analysis at main time points of the <i>P. falciparum</i> asexual life cycle.

<p>The time points color legend is indicated at the top left corner of the barplot. GO enrichment is indicated as stacked percentages.</p