ArticleBMC genomics2011
High-throughput 454 resequencing for allele discovery and recombination mapping in Plasmodium falciparum.
Article in BMC genomics, 2011. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 16 papers.
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Who cites it
16 citing papers in PubMed, 24 citations in OpenAlex.
- Whole Genome Sequencing Contributions and Challenges in Disease Reduction Focused on Malaria.Biology · 2022Review
- Indels, structural variation, and recombination drive genomic diversity in Plasmodium falciparum.Genome research · 2016Article
- Complete telomere-to-telomere de novo assembly of the Plasmodium falciparum genome through long-read (>11 kb), single molecule, real-time sequencing.DNA research : an international journal for rapid publication of reports on genes and genomes · 2016Article
- Review
- Imputation-based population genetics analysis of Plasmodium falciparum malaria parasites.PLoS genetics · 2015Article
- A MAT1-2 wild-type strain from Penicillium chrysogenum: functional mating-type locus characterization, genome sequencing and mating with an industrial penicillin-producing strain.Molecular microbiology · 2015Article
- DNA repair mechanisms and their biological roles in the malaria parasite Plasmodium falciparum.Microbiology and molecular biology reviews : MMBR · 2014Review
- Identification of pathogen genomic variants through an integrated pipeline.BMC bioinformatics · 2014Article
- Using genetic methods to define the targets of compounds with antimalarial activity.Journal of medicinal chemistry · 2013Review
- Assessment of the geographic origins of pinewood nematode isolates via single nucleotide polymorphism in effector genes.PloS one · 2013Article
- High-resolution genotyping and mapping of recombination and gene conversion in the protozoan Theileria parva using whole genome sequencing.BMC genomics · 2012Article
- Module-based subnetwork alignments reveal novel transcriptional regulators in malaria parasite Plasmodium falciparum.BMC systems biology · 2012Article
- Article
- The landscape of inherited and de novo copy number variants in a Plasmodium falciparum genetic cross.BMC genomics · 2011Article
- Rapid whole genome optical mapping of Plasmodium falciparum.Malaria journal · 2011Article
- An optimized microarray platform for assaying genomic variation in Plasmodium falciparum field populations.Genome biology · 2011Article
Corrections and comments
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Authors and funding
8 authors at 2 institutions in 2 countries.
Funding
Abstract
backgroundKnowledge of the origins, distribution, and inheritance of variation in the malaria parasite (Plasmodium falciparum) genome is crucial for understanding its evolution; however the 81% (A+T) genome poses challenges to high-throughput sequencing technologies. We explore the viability of the Roche 454 Genome Sequencer FLX (GS FLX) high throughput sequencing technology for both whole genome sequencing and fine-resolution characterization of genetic exchange in malaria parasites.
resultsWe present a scheme to survey recombination in the haploid stage genomes of two sibling parasite clones, using whole genome pyrosequencing that includes a sliding window approach to predict recombination breakpoints. Whole genome shotgun (WGS) sequencing generated approximately 2 million reads, with an average read length of approximately 300 bp. De novo assembly using a combination of WGS and 3 kb paired end libraries resulted in contigs ≤ 34 kb. More than 8,000 of the 24,599 SNP markers identified between parents were genotyped in the progeny, resulting in a marker density of approximately 1 marker/3.3 kb and allowing for the detection of previously unrecognized crossovers (COs) and many non crossover (NCO) gene conversions throughout the genome.
conclusionsBy sequencing the 23 Mb genomes of two haploid progeny clones derived from a genetic cross at more than 30× coverage, we captured high resolution information on COs, NCOs and genetic variation within the progeny genomes. This study is the first to resequence progeny clones to examine fine structure of COs and NCOs in malaria parasites.
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