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… 
Third generation sequencing revises the molecular karyotype for Toxoplasma gondii and identifies emerging copy number variants in sexual recombinants
TLDR
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.
Decoding The Nuclear Genome of The Human Pathogen Babesia duncani Shed Light on its Virulence, Drug Susceptibility and Evolution among Apicomplexa
TLDR
Detailed examination of the B. duncani genome and comparative genomic analyses identified new classes of candidate virulence factors, suitable antigens for diagnosis of active infection, and several attractive drug targets, thus enriching the pipeline of small molecules that could be developed as effective therapies for the treatment of human babesiosis.
Plasmodium knowlesi – Clinical Isolate Genome Sequencing to Inform Translational Same-Species Model System for Severe Malaria
TLDR
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.
Population Genomic Structure and Recent Evolution of Plasmodium knowlesi, Peninsular Malaysia
TLDR
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.
Plasmodium knowlesi: a superb in vivo nonhuman primate model of antigenic variation in malaria
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.
Getting close to nature – Plasmodium knowlesi reference genome sequences from contemporary clinical isolates
TLDR
De Novo assembled genomes of Plasmodium knowlesi generated using Nanopore long reads using statistical results from BUSCO, QUAST, Pomoxis and AGAT.
Plasmodium genomics: an approach for learning about and ending human malaria
TLDR
The genetics and genomics of human malarias have been analyzed and various population-level genetic and genomic surveys, together with transcriptomic and proteomic studies, have shown the importance of molecular approaches in supporting malaria elimination.
Comparative 3D genome organization in apicomplexan parasites
TLDR
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.
Changes in genome organization of parasite-specific gene families during the Plasmodium transmission stages
TLDR
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.
...
1
2
3
...

References

SHOWING 1-10 OF 64 REFERENCES
De novo assembly of the Aedes aegypti genome using Hi-C yields chromosome-length scaffolds
TLDR
The Hi-C method, which measures the distance between contact points within and between chromosomes for scaffold validation, was used to create a genome assembly for the mosquito Aedes aegypti, and assemblies indicate that almost all genomic rearrangements among these species occur within, rather than between, chromosome arms.
A SICAvar switching event in Plasmodium knowlesi is associated with the DNA rearrangement of conserved 3' non-coding sequences.
The genome of the simian and human malaria parasite Plasmodium knowlesi
TLDR
This is the first monkey malaria parasite genome to be described, and it provides an opportunity for comparison with the recently completed P. vivax genome and other sequenced Plasmodium genomes.
High-Quality Genome Assembly and Annotation for Plasmodium coatneyi, Generated Using Single-Molecule Real-Time PacBio Technology
TLDR
This is the first Plasmodium genome sequence reported to use only PacBio technology and has proven to be superior to short-read only approaches for this species.
Companion: a web server for annotation and analysis of parasite genomes
TLDR
The Companion web server is developed providing parasite genome annotation as a service using a reference-based approach and the use and performance is demonstrated by annotating two Leishmania and Plasmodium genomes as typical parasite cases and compared to manually annotated references.
Population genomic structure and adaptation in the zoonotic malaria parasite Plasmodium knowlesi
TLDR
Genome sequence analysis reveals that the zoonotic malaria parasite Plasmodium knowlesi consists of three highly divergent subpopulations, including two commonly seen in sympatric human clinical infections in Malaysian Borneo and five lines maintained in laboratory rhesus macaques after isolation in the 1960s from Peninsular Malaysia and the Philippines.
Redefining the expressed prototype SICAvar gene involved in Plasmodium knowlesi antigenic variation
TLDR
The prototype 205 SICAvar gene has been redefined to have a 12-exon structure, with an unusually large and repeat-laden intron separating two newly defined upstream exons and the bona fide 5'UTR from the remainder of the gene sequence.
Plasmodium knowlesi: a superb in vivo nonhuman primate model of antigenic variation in malaria
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.
Three-dimensional modeling of the P. falciparum genome during the erythrocytic cycle reveals a strong connection between genome architecture and gene expression.
TLDR
The results are indicative of a strong association between the P. falciparum spatial genome organization and gene expression, and the molecular processes involved in genome conformation dynamics could contribute to the discovery of novel antimalarial strategies.
...
1
2
3
4
5
...