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Parasitology. 2018 Jan;145(1):71-84. doi: 10.1017/S0031182017001329. Epub 2017 Jul 19.

PacBio assembly of a Plasmodium knowlesi genome sequence with Hi-C correction and manual annotation of the SICAvar gene family.

Author information

1
Emory Vaccine Center,Yerkes National Primate Research Center,Emory University,Atlanta, GA,USA.
2
Federal University of Minas Gerais,Belo Horizonte, MG,Brazil.
3
La Jolla Institute for Allergy and Immunology,La Jolla, CA 92037,USA.
4
Institute of Bioinformatics, University of Georgia,Athens, GA 30602,USA.
5
Center for Disease and Vector Research,Institute for Integrative Genome Biology,Department of Cell Biology & Neuroscience,University of California Riverside,CA 92521,USA.

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.

KEYWORDS:

Plasmodium knowlesi ; SICAvar ; Hi-C; MaHPIC; PacBio; annotation; antigenic variation; genome; sequence

PMID:
28720171
PMCID:
PMC5798397
DOI:
10.1017/S0031182017001329
[Indexed for MEDLINE]
Free PMC Article

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