SUMMARYPlasmodium 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.