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

@article{Lapp2017PacBioAO,
  title={PacBio assembly of a Plasmodium knowlesi genome sequence with Hi-C correction and manual annotation of the SICAvar gene family},
  author={Stacey A. Lapp and J. A. Geraldo and Jung-Ting Chien and Ferhat Ay and Suman Pakala and Gayani Batugedara and Jay C. Humphrey and Jeremy D. DeBarry and Karine G. Le Roch and Mary R. Galinski and Jessica C. Kissinger},
  journal={Parasitology},
  year={2017},
  volume={145},
  pages={71 - 84}
}
SUMMARY 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… 
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The first use of single molecule DNA sequencing is reported to generate near complete de novo genome assemblies for T. gondii and its near relative, N. caninum, and revising the molecular karyotype found that while the 13 chromosome karyotypes was conserved, it was determined that previously unidentified large scale translocation events occurred in T. rhoptry protein 5 and ROP38.
Molecular epidemiology and population genomics of Plasmodium knowlesi.
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A method to generate long-read third-generation Plasmodium genome sequence data from archived clinical samples using the MinION platform and it is proposed that by widely adopting this methodology important information on clinically relevant parasite diversity, including multiple gene family members, from geographically distinct study sites will emerge.
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Each subpopulation comprising P. knowlesi infections that were almost identical to each other throughout much of the genome, indicating separately maintained transmission and recent genetic isolation could evolve and present a broader health challenge in Asia.
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TLDR
An historical account of this topic is provided, while highlighting the potential for maximizing the use of P. knowlesi – macaque model systems and summarizing exciting new progress in this area of research.
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TLDR
De Novo assembled genomes of Plasmodium knowlesi generated using Nanopore long reads using statistical results from BUSCO, QUAST, Pomoxis and AGAT.
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The results suggest that genome organization in malaria parasites has been shaped by parasite-specific gene families and correlates with virulence, suggesting a potential link between genome organization and gene expression in more virulent pathogens.
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The results suggest that the three-dimensional genome structure is strongly connected with transcriptional activity of specific gene families throughout the life cycle of human malaria parasites.
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