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A new Plasmodium vivax reference genome for South American isolates

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dc.contributor.author De Meulenaere, Katlijn
dc.contributor.author Cuypers, Bart
dc.contributor.author Gamboa Vilela, Dionicia Baziliza
dc.contributor.author Laukens, Kris
dc.contributor.author Rosanas-Urgell, Anna
dc.date.accessioned 2023-12-07T22:33:23Z
dc.date.available 2023-12-07T22:33:23Z
dc.date.issued 2023
dc.identifier.uri https://hdl.handle.net/20.500.12866/14699
dc.description.abstract Background: Plasmodium 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. Results: This study presents a new high-quality assembly of a South American P. vivax isolate, referred to as PvPAM (P. vivax Peruvian AMazon). 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. Conclusions: Our 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. en_US
dc.language.iso eng
dc.publisher BioMed Central
dc.relation.ispartofseries BMC Genomics
dc.rights info:eu-repo/semantics/restrictedAccess
dc.rights.uri https://creativecommons.org/licenses/by-nc-nd/4.0/deed.es
dc.subject Plasmodium vivax en_US
dc.subject Genome assembly en_US
dc.subject PacBio sequencing en_US
dc.subject Reference genome en_US
dc.subject.mesh Plasmodium vivax
dc.subject.mesh Proteínas del Complejo de Importación de Proteínas Precursoras Mitocondriales
dc.subject.mesh Datos de Secuencia Molecular
dc.subject.mesh Genoma
dc.title A new Plasmodium vivax reference genome for South American isolates en_US
dc.type info:eu-repo/semantics/article
dc.identifier.doi https://doi.org/10.1186/s12864-023-09707-5
dc.relation.issn 1471-2164


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