A reference genome and methylome for the Plasmodium knowlesi A1-H.1 line

Ernest Diez Benavente,Paola Florez De Sessions,Robert W Moon,Munira Grainger,Anthony A Holder,Michael J Blackman,Cally Roper,Christopher J Drakeley,Arnab Pain,Colin J Sutherland,Martin L Hibberd,Susana Campino,Taane G Clark

doi:10.1016/j.ijpara.2017.09.008

Abstract

Plasmodium knowlesi, a common parasite of macaques, is recognised as a significant cause of human malaria in Malaysia. The P. knowlesi A1H1 line has been adapted to continuous culture in human erythrocytes, successfully providing an in vitro model to study the parasite. We have assembled a reference genome for the PkA1-H.1 line using PacBio long read combined with Illumina short read sequence data. Compared with the H-strain reference, the new reference has improved genome coverage and a novel description of methylation sites. The PkA1-H.1 reference will enhance the capabilities of the in vitro model to improve the understanding of P. knowlesi infection in humans.

Highlights

The P. knowlesi A1.H1 (PkA1-H.1) line was the first to be successfully adapted to continuous culture in human erythrocytes, providing an in vitro model suitable for genetic modification (Moon et al, 2009)
The high quality corrected contigs were ordered with Abacas software using the current Plasmodium knowlesi H strain (PKNH) reference, and manually checked to remove possible errors
The samples were aligned against the PkA1-H.1 reference using bwa-mem (Li and Durbin, 2009) and single nucleotide polymorphisms (SNPs) were called using the Samtools software suite (Li, 2011), from which a set of high quality SNPs was filtered using previously described methods (Samad et al, 2015; Campino et al, 2016)

Summary

Introduction

The P. knowlesi A1.H1 (PkA1-H.1) line was the first to be successfully adapted to continuous culture in human erythrocytes, providing an in vitro model suitable for genetic modification (Moon et al, 2009). PacBio data were available for the A1-H.1 clone, but were insufficient in themselves to lead to a complete genome i.e. single contig chromosomes (Moon et al, 2016). To assess the performance of the PkA1-H.1 reference, we aligned whole genome sequence data from 60 published human P. knowlesi isolates (Assefa et al, 2015; Pinheiro et al, 2015).

Results

Conclusion