Preprint Article Version 1 Preserved in Portico This version is not peer-reviewed

Long-Read Sequencing and De Novo Genome Assembly Pipeline of Two Plasmodium falciparum Clones (Pf3D7, PfW2) Using Only the PromethION Sequencer from Oxford Nanopore Technologies without Whole Genome Amplification

Océane Delandre
* ORCID logo ,
Ombeline Lamer
,
Jean-Marie Loreau
,
Nasserdine Papa Mze
ORCID logo ,
Isabelle Fonta
,
Joel Mosnier
,
Nicolas Gomez
,
Emilie Javelle
,
Bruno Pradines
ORCID logo
Version 1 : Received: 11 January 2024 / Approved: 12 January 2024 / Online: 12 January 2024 (07:01:51 CET)

A peer-reviewed article of this Preprint also exists.

Delandre, O.; Lamer, O.; Loreau, J.-M.; Papa Mze, N.; Fonta, I.; Mosnier, J.; Gomez, N.; Javelle, E.; Pradines, B. Long-Read Sequencing and De Novo Genome Assembly Pipeline of Two Plasmodium falciparum Clones (Pf3D7, PfW2) Using Only the PromethION Sequencer from Oxford Nanopore Technologies without Whole-Genome Amplification. Biology 2024, 13, 89. Delandre, O.; Lamer, O.; Loreau, J.-M.; Papa Mze, N.; Fonta, I.; Mosnier, J.; Gomez, N.; Javelle, E.; Pradines, B. Long-Read Sequencing and De Novo Genome Assembly Pipeline of Two Plasmodium falciparum Clones (Pf3D7, PfW2) Using Only the PromethION Sequencer from Oxford Nanopore Technologies without Whole-Genome Amplification. Biology 2024, 13, 89.

Abstract

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 gold-standard to sequence Plasmodium. Two clones of P.falciparum (Pf3D7 and PfW2) 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 Plasmodium with ONT Fastq only. De novo assembly revealed N50 lengths of 18,488 kb and 17,502 kb for the Pf3D7 and PfW2, respectively. The genome size was estimated at 23,235,407 base pairs for the Pf3D7 clone and 21,712,038 base pairs for the PfW2 clone. The average genome coverage depth was estimated at 787X and 653X for the Pf3D7 and PfW2 clones, respectively. This study proposes an assembly processing pipeline for the human Plasmodium genome using software’s adapted to large ONT data and the high AT percentage of Plasmodium. This search provides all the parameters, which have been optimized, for use with the software selected in the pipeline.

Keywords

Genome assembly; Plasmodium falciparum; Long-read sequencing; Nanopore; PromethION; Pf3D7; PfW2

Subject

Biology and Life Sciences, Parasitology

Copyright: This is an open access article distributed under the Creative Commons Attribution License which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.

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