TY - JOUR
T1 - Long-read genome assembly and gene model annotations for the rodent malaria parasite Plasmodium yoelii 17XNL
AU - Godin, Mitchell J.
AU - Sebastian, Aswathy
AU - Albert, Istvan
AU - Lindner, Scott E.
N1 - Funding Information:
This work was supported by awards from NIAID , National Institutes of Health ( R01AI123341 , R56AI123341 ) to S. E. L., NIGMS , National Institutes of Health ( T32GM125592 ) to M. J. G., and support to A. S. from the Huck Institutes of the Life Sciences . The content is solely the responsibility of the authors and does not necessarily represent the official views of the National Institutes of Health.
Funding Information:
We acknowledge the Penn State Genomics Core Facility–University Park for sequencing library preparations and conducting the PacBio and Illumina sequencing described in this study. We thank the Tanya Renner lab at Penn State for critical discussions on Nanopore sequencing. We thank New England Biolabs for early access to high-molecular-weight gDNA purification kits and their insights on the optimization of this process. We also thank members of the VEuPathDB and PlasmoDB.org teams for assistance with current data files and assemblies, Akhil Vaidya (Drexel University) for discussions about the Plasmodium mitochondrion, Photini Sinnis on discussions about CSP and its central repeat sequence, as well as the members of the Llinás and Lindner laboratories for critical discussions of this work. M. J. G. A. S. I. A. S. E. L. conceptualization; M. J. G. A. S. I. A. S. E. L. data curation; M. J. G. A. S. I. A. S. E. L. formal analysis; M. J. G. S. E. L. funding acquisition; M. J. G. A. S. investigation; M. J. G. A. S. I. A. S. E. L. methodology; I. A. S. E. L. project administration; I. A. S. E. L. resources; A. S. I. A. software; I. A. S. E. L. supervision; M. J. G. A. S. I. A. S. E. L. validation; M. J. G. A. S. I. A. S. E. L. visualization; M. J. G. A. S. A. I. S. E. L. writing–original draft; M. J. G. A. S. I. A. S. E. L. writing–reviewing and editing. This work was supported by awards from NIAID, National Institutes of Health (R01AI123341, R56AI123341) to S. E. L. NIGMS, National Institutes of Health (T32GM125592) to M. J. G. and support to A. S. from the Huck Institutes of the Life Sciences. The content is solely the responsibility of the authors and does not necessarily represent the official views of the National Institutes of Health.
Publisher Copyright:
© 2023 The Authors
PY - 2023/7
Y1 - 2023/7
N2 - Malaria causes >600 thousand fatalities each year, with most cases attributed to the human-infectious Plasmodium falciparum species. Many rodent-infectious Plasmodium species, like Plasmodium berghei and Plasmodium yoelii, have been used as model species that can expedite studies of this pathogen. P. yoelii is an especially good model for investigating the mosquito and liver stages of development because key attributes closely resemble those of P. falciparum. Because of its importance, in 2002 the 17XNL strain of P. yoelii was the first rodent malaria parasite to be sequenced. Although this was a breakthrough effort, the assembly consisted of >5000 contiguous sequences that adversely impacted the annotated gene models. While other rodent malaria parasite genomes have been sequenced and annotated since then, including the related P. yoelii 17X strain, the 17XNL strain has not. As a result, genomic data for 17X has become the de facto reference genome for the 17XNL strain while leaving open questions surrounding possible differences between the 17XNL and 17X genomes. In this work, we present a high-quality genome assembly for P. yoelii 17XNL using PacBio DNA sequencing. In addition, we use Nanopore and Illumina RNA sequencing of mixed blood stages to create complete gene models that include coding sequences, alternate isoforms, and UTR designations. A comparison of the 17X and this new 17XNL assembly revealed biologically meaningful differences between the strains due to the presence of coding sequence variants. Taken together, our work provides a new genomic framework for studies with this commonly used rodent malaria model species.
AB - Malaria causes >600 thousand fatalities each year, with most cases attributed to the human-infectious Plasmodium falciparum species. Many rodent-infectious Plasmodium species, like Plasmodium berghei and Plasmodium yoelii, have been used as model species that can expedite studies of this pathogen. P. yoelii is an especially good model for investigating the mosquito and liver stages of development because key attributes closely resemble those of P. falciparum. Because of its importance, in 2002 the 17XNL strain of P. yoelii was the first rodent malaria parasite to be sequenced. Although this was a breakthrough effort, the assembly consisted of >5000 contiguous sequences that adversely impacted the annotated gene models. While other rodent malaria parasite genomes have been sequenced and annotated since then, including the related P. yoelii 17X strain, the 17XNL strain has not. As a result, genomic data for 17X has become the de facto reference genome for the 17XNL strain while leaving open questions surrounding possible differences between the 17XNL and 17X genomes. In this work, we present a high-quality genome assembly for P. yoelii 17XNL using PacBio DNA sequencing. In addition, we use Nanopore and Illumina RNA sequencing of mixed blood stages to create complete gene models that include coding sequences, alternate isoforms, and UTR designations. A comparison of the 17X and this new 17XNL assembly revealed biologically meaningful differences between the strains due to the presence of coding sequence variants. Taken together, our work provides a new genomic framework for studies with this commonly used rodent malaria model species.
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U2 - 10.1016/j.jbc.2023.104871
DO - 10.1016/j.jbc.2023.104871
M3 - Article
C2 - 37247760
AN - SCOPUS:85162851371
SN - 0021-9258
VL - 299
JO - Journal of Biological Chemistry
JF - Journal of Biological Chemistry
IS - 7
M1 - 104871
ER -