Plasmodium falciparum
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ABSTRACT:
PROVIDER: PRJNA133917 | ENA |
REPOSITORIES: ENA
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Project description:We used a high-density tiling array to estimate genetic recombination rate among 32 independent recombinant progeny of a P. falciparum genetic cross (7G8 × GB4). We detected 3184 segregating multi-probe single-feature polymorphisms (mSFPs) and 638 recombination events (496 excluding those from subtelomeric regions). These data, in combination with results from 254 previously reported microsatellites, enabled us to construct a high-resolution genetic map. Comparing genetic and physical maps, we obtained an overall recombination rate of 9.6 kb/cM (12.8 kb/cM excluding subtelomeric regions) and identified 54 hotspots, some of which occurred in genes encoding surface antigens or proteins with repetitive motifs that might play a role in genetic recombination in the parasite. Motifs enriched in hotspots were also identified. In agreement with results from a previous cross (HB3 ´ Dd2), there was positive correlation between sizes of individual chromosomes and their recombination events. These results show that the P. falciparum genome is highly recombinogenic, providing an important genetic basis for parasite survival under various selection pressures. GC-rich repetitive motifs identified in the hotspot sequences may play a role in the high recombination frequency observed.
2011-03-16 | GSE25656 | GEO
Project description:We used a high-density tiling array to estimate genetic recombination rate among 32 independent recombinant progeny of a P. falciparum genetic cross (7G8 M-CM-^W GB4). We detected 3184 segregating multi-probe single-feature polymorphisms (mSFPs) and 638 recombination events (496 excluding those from subtelomeric regions). These data, in combination with results from 254 previously reported microsatellites, enabled us to construct a high-resolution genetic map. Comparing genetic and physical maps, we obtained an overall recombination rate of 9.6 kb/cM (12.8 kb/cM excluding subtelomeric regions) and identified 54 hotspots, some of which occurred in genes encoding surface antigens or proteins with repetitive motifs that might play a role in genetic recombination in the parasite. Motifs enriched in hotspots were also identified. In agreement with results from a previous cross (HB3 M-BM-4 Dd2), there was positive correlation between sizes of individual chromosomes and their recombination events. These results show that the P. falciparum genome is highly recombinogenic, providing an important genetic basis for parasite survival under various selection pressures. GC-rich repetitive motifs identified in the hotspot sequences may play a role in the high recombination frequency observed. Ten microgram of genomic DNA, extracted and purified from 3D7 (reference), thirty-two P. falciparum independent recombinant progeny of the 7G8 x GB4 cross, and the two parental lines (Hayton, 2008), were hybridized to the PFSANGER GenechipM-BM-. (Affymetrix, Inc., Santa Clara, CA, USA). The scanned image CEL files were first processed using the RMA method, then averaged and compared with reference genome 3D7, and lastly assigned either 7G8 or GB4 alleles based on similarities to the two parental lines. Total of 35 genomic DNA samples (biological replicates: 6 for 3D7, 4 for 7G8, 4 for GB4, and 2 for Pf_WE2). The supplementary file 'GSE25656_QuantNormData_Log2_AllSamples.txt' contains the RMA-normalized data for all of the samples. The supplementary files 'GSE25656_chr*' contain the parental allele assignment of each chromosome and include probe-level annotation.
2011-03-16 | E-GEOD-25656 | biostudies-arrayexpress
Project description:Plasmodium falciparum raw sequence data from genetic crosses
| PRJNA524855 | ENA
Project description:Transcriptomic Analysis of Cultured Sporozoites of P. falciparum RNA-seq reads from each of three developmental stages (2 replicates per sample) were mapped to the reference Plasmodium falciparum genome, and gene expression levels were calculated for each sample.
2013-12-03 | E-GEOD-52867 | biostudies-arrayexpress
Project description:ChIP-seq experiments were performed for the putative telomere repeat-binding factor (PfTRF) in the malaria parasite Plasmodium falciparum strain 3D7. The gene encoding this factor (PF3D7_1209300) was endogenously tagged with either a GFP- or a 3xHA-tag and these transgenic parasite lines were used in ChIP-sequencing experiments. Sequencing of the ChIP and input libraries showed enrichment of PfTRF at all telomere-repeat containing chromosome ends (reference genome Plasmodium falciparum 3D7 from PlasmoDB version 6.1) as well as in all upsB var promoters.In addition,PfTRF was enriched at seven additional, intra-chromosomal sites and called in the PfTRF-HA ChIP-seq only. Plasmodium falciparum 3D7 parasites were generated with -GFP or -3xHA C-terminal tagged TRF (PF3D7_1209300). Nuclei were isolated from formaldehyde cross-linked schizont-stage transgenic parasites and used to prepare chromatin. Chromatin immunoprecipitations were performed using mouse anti-GFP (Roche Diagnostics, #11814460001) or rat anti-HA 3F10 (Roche Diagnostics, #12158167001). Sequencing libraries were prepared according to a Plasmodium-optimized library preparation procedure including KAPA polymerase-mediated PCR amplification.
2016-07-15 | E-GEOD-76537 | biostudies-arrayexpress
Project description:To investigate the accumulation of non coding small RNAs we performed high throughput RNA sequencing on size selcted total RNA from malaria parasite Plasmodium falciparum
2018-08-22 | GSE107625 | GEO
Project description:Plasmodium falciparum Genome sequencing
| PRJNA278779 | ENA
Project description:Plasmodium falciparum Genome sequencing
| PRJNA253899 | ENA
Project description:Plasmodium falciparum Genome sequencing
| PRJNA359100 | ENA