Abstract
Plasmodium knowlesi has risen in importance as a zoonotic parasite that has been causing regular episodes of malaria throughout South East Asia. The P. knowlesi genome sequence generated in 2008 highlighted and confirmed many similarities and differences in Plasmodium species, including a global view of several multigene families, such as the large SICAvar multigene family encoding the variant antigens known as the schizont-infected cell agglutination proteins. However, repetitive DNA sequences are the bane of any genome project, and this and other Plasmodium genome projects have not been immune to the gaps, rearrangements and other pitfalls created by these genomic features. Today, long-read PacBio and chromatin conformation technologies are overcoming such obstacles. Here, based on the use of these technologies, we present a highly refined de novo P. knowlesi genome sequence of the Pk1(A+) clone. This sequence and annotation, referred to as the 'MaHPIC Pk genome sequence', includes manual annotation of the SICAvar gene family with 136 full-length members categorized as type I or II. This sequence provides a framework that will permit a better understanding of the SICAvar repertoire, selective pressures acting on this gene family and mechanisms of antigenic variation in this species and other pathogens.
Highlights
Plasmodium knowlesi is recognized as a zoonotic parasite and widespread public health threat in South East Asia, with acute and severe illness requiring hospitalization (Singh et al 2004; Singh and Daneshvar, 2013; Muller and Schlagenhauf, 2014; Ahmed and Cox-Singh, 2015; Wesolowski et al 2015)
A refined P. knowlesi genome sequence has been generated de novo from genomic DNA (gDNA) of the Pk1(A+) clone of the Malayan strain of this species
Both nuclear and organellar sequences were assembled from Pacific Biosciences (PacBio) reads
Summary
Plasmodium knowlesi is recognized as a zoonotic parasite and widespread public health threat in South East Asia, with acute and severe illness requiring hospitalization (Singh et al 2004; Singh and Daneshvar, 2013; Muller and Schlagenhauf, 2014; Ahmed and Cox-Singh, 2015; Wesolowski et al 2015). There has been a natural, increasing interest and momentum towards understanding the genetic, biological and pathogenic mechanisms that operate during P. knowlesi infections both in humans and non-human primates (Cox-Singh and Culleton, 2015; Millar and Cox-Singh, 2015) To fight this zoonosis, there is a need to understand the geographical distribution of the parasite and its dynamics to enable local and global actions for rapid treatment and work to break the cycle of transmission (Moyes et al 2014; Shearer et al 2016; Barber et al 2017). An accurate reference genome sequence can be important for vaccine and drug target discovery, and critical for certain basic biology studies This is especially the case for studying the evolution of complex multigene families, their regulation and antigenic variation.
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