Long-Read Sequencing and De Novo Genome Assembly Pipeline of Two Plasmodium falciparum Clones ( Pf 3D7, Pf W2) Using Only the PromethION Sequencer from Oxford Nanopore Technologies without Whole-Genome Amplification

Antimalarial drug resistance has become a real public health problem despite WHO measures. New sequencing technologies make it possible to investigate genomic variations associated with resistant phenotypes at the genome-wide scale. Based on the use of hemisynthetic nanopores, the PromethION technol...

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Bibliographic Details
Published in:Biology (Basel, Switzerland) Switzerland), 2024-01, Vol.13 (2), p.89
Main Authors: Delandre, Océane, Lamer, Ombeline, Loreau, Jean-Marie, Papa Mze, Nasserdine, Fonta, Isabelle, Mosnier, Joel, Gomez, Nicolas, Javelle, Emilie, Pradines, Bruno
Format: Article
Language:English
Subjects:
Antimalarial agents
Antiparasitic agents
Bacteriology
Base pairs
Bioinformatics
Cardiology and cardiovascular system
Chromosomes
Cloning
Drug resistance
Emerging diseases
Genetic engineering
genome assembly
Genomes
Genomics
Human health and pathology
Infectious diseases
Life Sciences
long-read sequencing
Malaria
Microbiology and Parasitology
Mitochondria
nanopore
Parasitology
Pf3D7
Phenotypes
Phenotypic variations
Plasmodium
Plasmodium falciparum
PromethION
Proteins
Public health
Software
Virology
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Summary:Antimalarial drug resistance has become a real public health problem despite WHO measures. New sequencing technologies make it possible to investigate genomic variations associated with resistant phenotypes at the genome-wide scale. Based on the use of hemisynthetic nanopores, the PromethION technology from Oxford Nanopore Technologies can produce long-read sequences, in contrast to previous short-read technologies used as the gold standard to sequence Plasmodium. Two clones of ( 3D7 and W2) were sequenced in long-read using the PromethION sequencer from Oxford Nanopore Technologies without genomic amplification. This made it possible to create a processing analysis pipeline for human with ONT Fastq only. assembly revealed N50 lengths of 18,488 kb and 17,502 kb for the 3D7 and W2, respectively. The genome size was estimated at 23,235,407 base pairs for the clone and 21,712,038 base pairs for the W2 clone. The average genome coverage depth was estimated at 787X and 653X for the 3D7 and W2 clones, respectively. This study proposes an assembly processing pipeline for the human genome using software adapted to large ONT data and the high AT percentage of . This search provides all the parameters which were optimized for use with the software selected in the pipeline.
ISSN:2079-7737
2079-7737
DOI:10.3390/biology13020089