First Full Draft Genome Sequence of Plasmodium brasilianum

Abstract

ABSTRACT

Plasmodium malariae is a protozoan parasite that can cause human malaria. The simian parasite Plasmodium brasilianum infects New World monkeys from Latin America and is morphologically indistinguishable from P. malariae. Here, we report the first full draft genome sequence for P. brasilianum.

GENOME ANNOUNCEMENT

Human malaria can be caused by five parasite species called Plasmodium falciparum, Plasmodium vivax, Plasmodium knowlesi, Plasmodium ovale, and Plasmodium malariae. Reference genome sequences are now published for the first three species (1–3), and draft genome sequences for the latter three species have been made available online at http://biorxiv.org/content/early/2016/05/12/052696). P. brasilianum greatly resembles the quartan P. malariae morphologically, but early experimental cross-species infections were unsuccessful and thus were classified as distinct species (4). Recent work from the Venezuelan Amazon, however, has suggested that P. brasilianum is likely able to infect humans (5). Here, we report the first draft genome sequence for P. brasilianum based on Illumina short-read sequencing technology.

Genomic DNA was extracted from ex vivo mature schizont stage parasites of the Bolivian I strain of P. brasilianum using the Qiagen DNA blood kit (catalog no. 51104; Qiagen, CA, USA). Four separate genomic DNA libraries were prepared using the NEBNext Ultra library prep kit (catalog no. E7370S; New England BioLabs, MA, USA). Two of the libraries were sequenced on two separate runs on the MiSeq using the MiSeq 500-cycle reagent kit (catalog no. MS-102-2003; Illumina, CA). The remaining two libraries were sequenced on two separate runs on the HiSeq 2500 using the HiSeq 150-cycle reagent kit (FC-410-1002). For initial data quality filtering, BBduk (https://sourceforge.net/projects/bbmap/) was used to trim 5′ and 3′ ends (i.e., quality < 35), remove PhiX, sequencing indices, and adaptors, and discard reads less than 50 bp. Post-quality trim, potential host DNA contamination was removed using the Saimiri monkey reference genome (GenBank accession no. 1GCA_000235385.1). A total of 420,061,864 paired-end reads remained with a Q20 (i.e., base call accuracy) of 99.9% or greater from all four sequencing runs. Nuclear genome assembly of combined filtered reads was performed using CLC Genomics Workbench version 9.0. Quality assessment of the full genome assembly was done using QUAST (6). Gene prediction was performed using GeneMark-ES (7). The mitochondrial and apicoplast genomes were assembled using the Geneious de novo assembler using the circularize contigs with matching regions option (8). The P. malariae reference mitochondrial (GenBank accession no. AB354570) and apicoplast (GenBank accession no. AB649418) genomes were used to annotate all the genes for the respective P. brasilianum genomes. Both the mitochondrial and apicoplast genomes were 99.70% identical to the published P. malariae genomes.

The final assembly of the nuclear genome consisted of 963 contigs (mean coverage, 70×) comprising 31,73,3118 bp, with an N₅₀ of 49,088 bp and G+C content of 25%. The largest contig was 344,535 bp. A total of 6,050 protein-encoding genes were predicted using GeneMark-ES. The complete P. brasilianum mitochondrial and apicoplast genomes are also included in this report.

Accession number(s).

This whole-genome shotgun project has been deposited at DDBJ/ENA/GenBank under the accession no. MKLA00000000. The version described in this paper is version MKLA01000000.