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    Comprehensive Evaluation of Toxoplasma gondii VEG and Neospora caninum LIV Genomes with Tachyzoite Stage Transcriptome and Proteome Defines Novel Transcript Features

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    Type
    Article
    Authors
    Ramaprasad, Abhinay cc
    Mourier, Tobias
    Naeem, Raeece cc
    Malas, Tareq Majed Yasin cc
    Moussa, Ehab
    Panigrahi, Aswini Kumar
    Vermont, Sarah J.
    Otto, Thomas D.
    Wastling, Jonathan
    Pain, Arnab cc
    KAUST Department
    Biological and Environmental Sciences and Engineering (BESE) Division
    Bioscience Core Lab
    Bioscience Program
    Computer Science Program
    Computer, Electrical and Mathematical Sciences and Engineering (CEMSE) Division
    Pathogen Genomics Laboratory
    Date
    2015-04-13
    Permanent link to this record
    http://hdl.handle.net/10754/550412
    
    Metadata
    Show full item record
    Abstract
    Toxoplasma gondii is an important protozoan parasite that infects all warm-blooded animals and causes opportunistic infections in immuno-compromised humans. Its closest relative, Neospora caninum, is an important veterinary pathogen that causes spontaneous abortion in livestock. Comparative genomics of these two closely related coccidians has been of particular interest to identify genes that contribute to varied host cell specificity and disease. Here, we describe a manual evaluation of these genomes based on strand-specific RNA sequencing and shotgun proteomics from the invasive tachyzoite stages of these two parasites. We have corrected predicted structures of over one third of the previously annotated gene models and have annotated untranslated regions (UTRs) in over half of the predicted protein-coding genes. We observe distinctly long UTRs in both the organisms, almost four times longer than other model eukaryotes. We have also identified a putative set of cis-natural antisense transcripts (cis-NATs) and long intergenic non-coding RNAs (lincRNAs). We have significantly improved the annotation quality in these genomes that would serve as a manually curated dataset for Toxoplasma and Neospora research communities.
    Citation
    Ramaprasad A, Mourier T, Naeem R, Malas TB, Moussa E, et al. (2015) Comprehensive Evaluation of Toxoplasma gondii VEG and Neospora caninum LIV Genomes with Tachyzoite Stage Transcriptome and Proteome Defines Novel Transcript Features. PLoS ONE 10(4): e0124473. doi:10.1371/journal.pone.0124473
    Publisher
    Public Library of Science (PLoS)
    Journal
    PLoS ONE
    DOI
    10.1371/journal.pone.0124473
    PubMed ID
    25875305
    PubMed Central ID
    PMC4395442
    Additional Links
    http://dx.plos.org/10.1371/journal.pone.0124473
    Relations
    Is Supplemented By:
    • [Bioproject]
      Title: This is a genome assembly third party annotation of Neospora caninum LIV strain based on strand-specific RNA-sequencing and manual re-annotation identifying novel features of UTRs and non-coding transcripts.Publication Date: 2015-02-26. bioproject: PRJEB7872 Handle: 10754/666436
    • [Bioproject]
      Title: This is a genome assembly third party annotation of Toxoplasma gondii VEG strain based on strand-specific RNA-sequencing and manual re-annotation identifying novel features of UTRs and non-coding transcripts.Publication Date: 2015-02-26. bioproject: PRJEB7873 Handle: 10754/666442
    ae974a485f413a2113503eed53cd6c53
    10.1371/journal.pone.0124473
    Scopus Count
    Collections
    Articles; Biological and Environmental Science and Engineering (BESE) Division; Bioscience Program; Computer Science Program; Bioscience Core Lab; Computer, Electrical and Mathematical Science and Engineering (CEMSE) Division

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