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. 2015 Apr 13;10(4):e0124473.
doi: 10.1371/journal.pone.0124473. eCollection 2015.

Comprehensive evaluation of Toxoplasma gondii VEG and Neospora caninum LIV genomes with tachyzoite stage transcriptome and proteome defines novel transcript features

Abhinay Ramaprasad  1 , Tobias Mourier  2 , Raeece Naeem  1 , Tareq B Malas  1 , Ehab Moussa  1 , Aswini Panigrahi  3 , Sarah J Vermont  4 , Thomas D Otto  5 , Jonathan Wastling  4 , Arnab Pain  1
Affiliations

Comprehensive evaluation of Toxoplasma gondii VEG and Neospora caninum LIV genomes with tachyzoite stage transcriptome and proteome defines novel transcript features

Abhinay Ramaprasad et al. PLoS One. .

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.

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Conflict of interest statement

Competing Interests: The authors have declared that no competing interests exist.

Figures

Fig 1
Fig 1. Summary of the manually curation of TgVEG and NcLIV (ToxoDb v8.0) genes.
A gene model was “corrected” by adding/deleting exons or altering their exon-intron boundaries to conform to the transcript and peptide evidence. The corrected genes also include the models that were either “split” into two separate genes or “merged” into a single gene based on transcript splice-site evidence. “New” genes were annotated in open reading frames with clear expression evidence. Genes that lacked expression evidence and overlapped with an expressed gene model were considered spurious and “deleted”.
Fig 2
Fig 2. Qualitative and quantitative assessment of manually re-evaluated genomes.
(A) We took confidence scores of Pfam domain hits (Pfam database v 26.0) as a rough indicator of the annotation quality and compared the e-value scores of Pfam domains before and after curation. Repetitive domains were omitted and the copy with the lowest e-value score is used for comparison. A 10-fold change in the e-value was considered as a significant change. While the e-values of Pfam domains in unchanged genes remain the same, we find a general increase in Pfam domain hit significance (decreasing e-values) after our curation (orange). We also find new Pfam domain hits appearing in the corrected genes (green) and in newly created genes (red). (B) Quantitative assessment of manual curation. Functional domain content of a genome is a crude indicator of annotation quality; therefore we compared the proportion of genes having a domain hit from InterProScan (grey) to genes without any domains (black). We find a ~20% increase in genes with functional domains after curation in TgVEG and ~10% in NcLIV genome.
Fig 3
Fig 3. Long untranslated regions and putative anti-sense non-coding RNAs in TgVEG and NcLIV.
(A) Length distribution of 5’UTRs, 3’UTRs and CDS in Toxoplasma gondii, Neospora caninum, Schizosaccharomyces pombe, Arabidopsis thaliana, Caenorhabditis elegans, Drosophila melanogaster and Homo sapiens. 5’UTRs are found to be strikingly large in the parasites, almost 4 times higher than other eukaryotes. 3’UTRs are comparable to those in human and longer than other eukaryotes. (B) Sequence conservation across UTRs and their flanking intergenic regions. UTR regions are generally more conserved than their flanking intergenic regions. (C) Log abundance ratio of antisense non-coding RNA (ancRNA) and sense coding mRNA pair versus sense coding RNA. There is an inverse relation between abundances of ancRNA and their sense mRNA counterpart.
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References

    1. Jones JL, Kruszon-Moran D, Wilson M, McQuillan G, Navin T, McAuley JB. Toxoplasma gondii infection in the United States: seroprevalence and risk factors. Am J Epidemiol. 2001;154: 357–365. - PubMed
    1. Kim K, Weiss LM. Toxoplasma gondii: the model apicomplexan. Int J Parasitol. 2004;34: 423–432. - PMC - PubMed
    1. Trees AJ, Davison HC, Innes EA, Wastling JM. Towards evaluating the economic impact of bovine neosporosis. Int J Parasitol. 1999;29: 1195–1200. - PubMed
    1. Reid A, Vermont S, Cotton J, Harris D, Hill-Cawthorne G, Könen-Waisman S, et al. Comparative genomics of the apicomplexan parasites Toxoplasma gondii and Neospora caninum: Coccidia differing in host range and transmission strategy. PLoS pathogens. 2012;8. - PMC - PubMed
    1. Gajria B, Bahl A, Brestelli J, Dommer J, Fischer S, Gao X, et al. ToxoDB: an integrated Toxoplasma gondii database resource. Nucleic acids research. 2008;36: D553–556. - PMC - PubMed

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Grants and funding

This project was supported by KAUST Faculty Base Research Funding (BRF) and KAUST-Cambridge Academic Excellence Alliance (AEA) Grant (7000000080) to AP. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.

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