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

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

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