ArticleDNA research : an international journal for rapid publication of reports on genes and genomes2016
Complete telomere-to-telomere de novo assembly of the Plasmodium falciparum genome through long-read (>11 kb), single molecule, real-time sequencing.
Article in DNA research : an international journal for rapid publication of reports on genes and genomes, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 31 papers.
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Who cites it
31 citing papers in PubMed.
- Development of an Oxford nanopore sequencing technology-based whole genome sequencing method for Plasmodium falciparum to support malaria molecular surveillance.Scientific reports · 2026Article
- Review
- Single-Molecule Real-Time Sequencing for Identifying Sexual-Dimorphism-Related Transcriptomes and Genes in the Chinese Soft-Shelled Turtle (Animals : an open access journal from MDPI · 2023Article
- LexicHash: sequence similarity estimation via lexicographic comparison of hashes.Bioinformatics (Oxford, England) · 2023Article
- An optimized GATK4 pipeline for Plasmodium falciparum whole genome sequencing variant calling and analysis.Malaria journal · 2023Article
- An Optimized GATK4 Pipeline for Plasmodium falciparum Whole Genome Sequencing Variant Calling and Analysis.Research square · 2023Article
- Whole Genome Sequencing Contributions and Challenges in Disease Reduction Focused on Malaria.Biology · 2022Review
- Alternative Splicing Landscape of Small Brown Planthopper and Different Response of JNK2 Isoforms to Rice Stripe Virus Infection.Journal of virology · 2022Article
- Population genomics in neglected malaria parasites.Frontiers in microbiology · 2022Review
- Long-read assembly and comparative evidence-based reanalysis ofGenome research · 2022Article
- Transcriptome analysis and molecular mechanism of linseed (Linum usitatissimum L.) drought tolerance under repeated drought using single-molecule long-read sequencing.BMC genomics · 2021Article
- A hybrid correcting method considering heterozygous variations by a comprehensive probabilistic model.BMC genomics · 2020Article
- Refining the transcriptome of the human malaria parasite Plasmodium falciparum using amplification-free RNA-seq.BMC genomics · 2020Article
- Performance difference of graph-based and alignment-based hybrid error correction methods for error-prone long reads.Genome biology · 2020Article
- Discovery of a new predominant cytosine DNA modification that is linked to gene expression in malaria parasites.Nucleic acids research · 2020Article
- Strains used in whole organism Plasmodium falciparum vaccine trials differ in genome structure, sequence, and immunogenic potential.Genome medicine · 2020Article
- Single-molecule real-time sequencing facilitates the analysis of transcripts and splice isoforms of anthers in Chinese cabbage (Brassica rapa L. ssp. pekinensis).BMC plant biology · 2019Article
- Comprehensive evaluation of non-hybrid genome assembly tools for third-generation PacBio long-read sequence data.Briefings in bioinformatics · 2019Article
- Common workflow language (CWL)-based software pipeline for de novo genome assembly from long- and short-read data.GigaScience · 2019Article
- A comparative evaluation of hybrid error correction methods for error-prone long reads.Genome biology · 2019Article
Corrections and comments
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Authors and funding
8 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
The application of next-generation sequencing to estimate genetic diversity of Plasmodium falciparum, the most lethal malaria parasite, has proved challenging due to the skewed AT-richness [∼80.6% (A + T)] of its genome and the lack of technology to assemble highly polymorphic subtelomeric regions that contain clonally variant, multigene virulence families (Ex: var and rifin). To address this, we performed amplification-free, single molecule, real-time sequencing of P. falciparum genomic DNA and generated reads of average length 12 kb, with 50% of the reads between 15.5 and 50 kb in length. Next, using the Hierarchical Genome Assembly Process, we assembled the P. falciparum genome de novo and successfully compiled all 14 nuclear chromosomes telomere-to-telomere. We also accurately resolved centromeres [∼90-99% (A + T)] and subtelomeric regions and identified large insertions and duplications that add extra var and rifin genes to the genome, along with smaller structural variants such as homopolymer tract expansions. Overall, we show that amplification-free, long-read sequencing combined with de novo assembly overcomes major challenges inherent to studying the P. falciparum genome. Indeed, this technology may not only identify the polymorphic and repetitive subtelomeric sequences of parasite populations from endemic areas but may also evaluate structural variation linked to virulence, drug resistance and disease transmission.
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