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2024-01-01
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PACBIO ASSEMBLY OF A PLASMODIUM KNOWLESI GENOME SEQUENCE WITH HI-C CORRECTION AND MANUAL ANNOTATION OF THE SIC AVAR GENE FAMILY
SICAvar
Hi-C
MaHPIC
PacBio
annotation
antigenic variation
genome
sequence
Author
Affilliation
Emory Vaccine Center. Yerkes National Primate Research Center. Emory University. Atlanta, GA, USA
Universidade Federal de Minas Gerais. Belo Horizonte, MG,Brazil/Fundação Oswaldo Cruz. Instituto René . Belo Horizonte, MG,Brazil.
Emory Vaccine Center. Yerkes National Primate Research Center. Emory University. Atlanta, GA, USA/Department of Mathematics and Computer Science. Emory University. Atlanta, GA, USA
La Jolla Institute for Allergy and Immunology. La Jolla. CA. USA
Institute of Bioinformatics. University of Georgia. Athens, GA, USA/Center for Tropical and Emerging Global Diseases. University of Georgia. Athens, GA,USA
Center for Disease and Vector Research. Institute for Integrative Genome Biology., Department of Cell Biology & Neuroscience. University of California. Riverside, CA,USA
Institute of Bioinformatics. University of Georgia. Athens, GA, USA/Center for Tropical and Emerging Global Diseases. University of Georgia. Athens, GA,USA
Malaria Host-Pathogen Interaction Center.
Institute of Bioinformatics. University of Georgia. Athens, GA, USA/Center for Tropical and Emerging Global Diseases. University of Georgia. Athens, GA,USA
Center for Disease and Vector Research. Institute for Integrative Genome Biology., Department of Cell Biology & Neuroscience. University of California. Riverside, CA,USA
Emory Vaccine Center. Yerkes National Primate Research Center. Emory University. Atlanta, GA, USA/Department of Mathematics and Computer Science. Emory University. Atlanta, GA, USA/ Division of Infectious Diseases. Department of Medicine. Emory University. Atlanta, GA,USA
Institute of Bioinformatics. University of Georgia. Athens, GA, USA/Center for Tropical and Emerging Global Diseases. University of Georgia. Athens, GA,USA/Department of Genetics. University of Georgia. Athens, GA, USA
Universidade Federal de Minas Gerais. Belo Horizonte, MG,Brazil/Fundação Oswaldo Cruz. Instituto René . Belo Horizonte, MG,Brazil.
Emory Vaccine Center. Yerkes National Primate Research Center. Emory University. Atlanta, GA, USA/Department of Mathematics and Computer Science. Emory University. Atlanta, GA, USA
La Jolla Institute for Allergy and Immunology. La Jolla. CA. USA
Institute of Bioinformatics. University of Georgia. Athens, GA, USA/Center for Tropical and Emerging Global Diseases. University of Georgia. Athens, GA,USA
Center for Disease and Vector Research. Institute for Integrative Genome Biology., Department of Cell Biology & Neuroscience. University of California. Riverside, CA,USA
Institute of Bioinformatics. University of Georgia. Athens, GA, USA/Center for Tropical and Emerging Global Diseases. University of Georgia. Athens, GA,USA
Malaria Host-Pathogen Interaction Center.
Institute of Bioinformatics. University of Georgia. Athens, GA, USA/Center for Tropical and Emerging Global Diseases. University of Georgia. Athens, GA,USA
Center for Disease and Vector Research. Institute for Integrative Genome Biology., Department of Cell Biology & Neuroscience. University of California. Riverside, CA,USA
Emory Vaccine Center. Yerkes National Primate Research Center. Emory University. Atlanta, GA, USA/Department of Mathematics and Computer Science. Emory University. Atlanta, GA, USA/ Division of Infectious Diseases. Department of Medicine. Emory University. Atlanta, GA,USA
Institute of Bioinformatics. University of Georgia. Athens, GA, USA/Center for Tropical and Emerging Global Diseases. University of Georgia. Athens, GA,USA/Department of Genetics. University of Georgia. Athens, GA, 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 knowlesiSICAvar
Hi-C
MaHPIC
PacBio
annotation
antigenic variation
genome
sequence
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