The First Complete Genome of the Simian Malaria Parasite Plasmodium brasilianum

Authors

Marko Bajic, United States Centers for Disease Control and Prevention
Shashidhar Ravishankar, Fred Hutchinson Cancer Research Center
Mili Sheth, United States Centers for Disease Control and Prevention
Lori A. Rowe, United States Centers for Disease Control and Prevention, Tulane National Primate Research Center
M. Andreina Pacheco, Temple University
Dhruviben S. Patel, United States Centers for Disease Control and Prevention
Dhwani Batra, United States Centers for Disease Control and Prevention
Vladimir Loparev, United States Centers for Disease Control and Prevention
Christian Olsen, Centers for Disease Control and Prevention
Ananias A. Escalante, Temple UniversityFollow
Fredrik Vannberg, Georgia Institute of Technology
Venkatachalam Udhayakumar, United States Centers for Disease Control and Prevention
John W. Barnwell, United States Centers for Disease Control and Prevention
Eldin Talundzic, United States Centers for Disease Control and Prevention

ORCID IDs

Escalante 0000-0002-1532-3430

Document Type

Article

Date of this Version

11-17-2022

Citation

Scientific Reports (2022) 12: 19802

doi: 10.1038/s41598-022-20706-6

Comments

United States government work, public domain

Abstract

Naturally occurring human infections by zoonotic Plasmodium species have been documented for P. knowlesi, P. cynomolgi, P. simium, P. simiovale, P. inui, P. inui-like, P. coatneyi, and P. brasilianum. Accurate detection of each species is complicated by their morphological similarities with other Plasmodium species. PCR-based assays offer a solution but require prior knowledge of adequate genomic targets that can distinguish the species. While whole genomes have been published for P. knowlesi, P. cynomolgi, P. simium, and P. inui, no complete genome for P. brasilianum has been available. Previously, we reported a draft genome for P. brasilianum, and here we report the completed genome for P. brasilianum. The genome is 31.4 Mb in size and comprises 14 chromosomes, the mitochondrial genome, the apicoplast genome, and 29 unplaced contigs. The chromosomes consist of 98.4% nucleotide sites that are identical to the P. malariae genome, the closest evolutionarily related species hypothesized to be the same species as P. brasilianum, with 41,125 non-synonymous SNPs (0.0722% of genome) identified between the two genomes. Furthermore, P. brasilianum had 4,864 (82.1%) genes that share 80% or higher sequence similarity with 4,970 (75.5%) P. malariae genes. This was demonstrated by the nearly identical genomic organization and multiple sequence alignments for the merozoite surface proteins msp3 and msp7. We observed a distinction in the repeat lengths of the circumsporozoite protein (CSP) gene sequences between P. brasilianum and P. malariae. Our results demonstrate a 97.3% pairwise identity between the P. brasilianum and the P. malariae genomes. These findings highlight the phylogenetic proximity of these two species, suggesting that P. malariae and P. brasilianum are strains of the same species, but this could not be fully evaluated with only a single genomic sequence for each species.