Biology subjects

De Meulenaere, K.

Publications and source records attributed to De Meulenaere, K..

3 recordsLinked to original sources

bioRxiv2026

A Plasmodium knowlesi A1-H.1 transcriptome time course focusing on the late asexual blood stages

BackgroundThe zoonotic parasite Plasmodium knowlesi is closely related to Plasmodium vivax, the second leading cause of human malaria. P. knowlesi line A1-H.1 can be maintained in human erythrocytes and is an experimental model for P. vivax biology. We present the first transcriptome time-course of the intraerythrocytic developmental cycle (IDC) of P. knowlesi A1-H.1 grown in human normocytes. ResultsBulk RNA-sequencing was performed at five IDC stages using tightly synchronised cultures, enabling identification of constitutively expressed genes and stage-specific biomarkers, and investigation of temporal expression patterns of multigene families. Comparative analysis with P. vivax orthologues revealed strong genome-wide conservation of temporal expression. Analysis of invasion-associated genes and ApiAP2 transcription factors identified genes with conserved expression patterns for which P. knowlesi is likely a good model to study the P. vivax gene. To support comparative analyses, we developed an open-access interactive webtool to explore and visualise P. knowlesi - P. vivax orthologue expression across the IDC. ConclusionsThis time-course dataset provides a reference transcriptome framework for P. knowlesi A1-H.1 and a resource for comparative Plasmodium biology. The interactive webtool facilitates rapid identification of candidate genes with conserved temporal expression, streamlining functional studies in which P. knowlesi A1-H.1 serves as a model for P. vivax.

genomics↗

bioRxiv2023

A new Plasmodium vivax reference genome for South American isolates

BackgroundPlasmodium vivax is the second most important cause of human malaria worldwide, and accounts for the majority of malaria cases in South America. A high-quality reference genome exists for Papua Indonesia (PvP01) and Thailand (PvW1), but is lacking for South America. A reference genome specifically for South America would be beneficial though, as P. vivax is a genetically diverse parasite with geographical clustering. ResultsThis study presents a new high-quality assembly of a South American P. vivax isolate, referred to as PvPAM. The genome was obtained from a low input patient sample from the Peruvian Amazon and sequenced using PacBio technology, resulting in a highly complete assembly with 6497 functional genes. Telomeric ends were present in 17 out of 28 chromosomal ends, and additional (sub)telomeric regions are present in 12 unassigned contigs. A comparison of multigene families between PvPAM and the PvP01 genome revealed remarkable variation in vir genes, and the presence of merozoite surface proteins (MSP) 3.6 and 3.7. Three dhfr and dhps drug resistance associated mutations are present in PvPAM, similar to those found in other Peruvian isolates. Mapping of publicly available South American whole genome sequencing (WGS) data to PvPAM resulted in significantly fewer variants and truncated reads compared to the use of PvP01 or PvW1 as reference genomes. To minimize the number of core genome variants in non-South American samples, PvW1 is most suited for Southeast Asian isolates, both PvPAM and PvW1 are suited for South Asian isolates, and PvPAM is recommended for African isolates. Interestingly, non-South American samples still contained the least subtelomeric variants when mapped to PvPAM, indicating high quality of the PvPAM subtelomeric regions. ConclusionsOur findings show that the PvPAM reference genome more accurately represents South American P. vivax isolates in comparison to PvP01 and PvW1. In addition, PvPAM has a high level of completeness, and contains a similar number of annotated genes as PvP01 or PvW1. The PvPAM genome therefore will be a valuable resource to improve future genomic analyses on P. vivax isolates from the South American continent.

genetics↗

bioRxiv2022

Selective whole-genome sequencing of Plasmodium parasites directly from blood samples by Nanopore adaptive sampling

BackgroundWhole-genome sequencing (WGS) is becoming an increasingly popular tool to study the population genetics and drug resistance of Plasmodium spp. However, the predominance of human DNA in a malaria patient blood sample requires time-consuming lab procedures to filter out human DNA or enrich Plasmodium DNA. Here, we investigated the potential of adaptive sampling to enrich for Plasmodium DNA while sequencing unenriched patient blood samples on a minION device. ResultsTo compare adaptive sampling versus regular sequencing, a dilution series consisting of 0% up to 100% P. falciparum DNA in human DNA was sequenced. Half of the flowcell channels were run in adaptive sampling mode, enriching for the P. falciparum reference genome, resulting in a 3.2 fold enrichment of P. falciparum bases on average. Samples with a lower concentration of parasite DNA had a higher enrichment potential. We confirmed these findings by sequencing two P. falciparum patient blood samples with common levels of parasitaemia (0.1% and 0.2%). The estimated enrichment was 3.9 and 5.8, which was sufficient to cover at least 97% of the P. falciparum reference genome at a median depth of 20 (highest parasitaemia) or 5 (lowest parasitaemia). A comparison of 38 drug resistance variants (WHO) obtained via adaptive sequencing or Sanger sequencing showed a high concordance between the two methods, suggesting that the obtained sequencing data is of sufficient quality to address common clinical research questions for patients with parasitaemias of 0.1% and higher. ConclusionsOur results demonstrate that adaptive Nanopore sequencing has the potential to replace more time-consuming Plasmodium-enrichment protocols and sequence directly from patient blood, given further improvements in cost-efficiency.

microbiology↗