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

• Published in: PloS one 2015-04, Vol.10 (4), p.e0124473-e0124473
• Main Authors: Ramaprasad, Abhinay, Mourier, Tobias, Naeem, Raeece, Malas, Tareq B, Moussa, Ehab, Panigrahi, Aswini, Vermont, Sarah J, Otto, Thomas D, Wastling, Jonathan, Pain, Arnab
• Format: Article
• Language: English
• Subjects: Analysis; Animals; Annotations; Antisense; Antisense RNA; Coccidiosis - parasitology; Coccidiosis - transmission; Eukaryotes; Evaluation; Gene expression; Gene Expression Regulation; Gene sequencing; Genes; Genome, Protozoan; Genomes; Genomics; Genomics - methods; Health aspects; High-Throughput Nucleotide Sequencing - methods; Homeotherms; Host-Parasite Interactions; Infectious Disease Transmission, Vertical; Livestock; Mathematical models; Miscarriage; Neospora - genetics; Neospora - metabolism; Neospora - pathogenicity; Parasites; Plasmodium falciparum; Proteome - analysis; Proteomics; Protozoa; Regulatory Sequences, Nucleic Acid - genetics; Ribonucleic acid; RNA; RNA, Long Noncoding - genetics; Toxoplasma - genetics; Toxoplasma - metabolism; Toxoplasma - pathogenicity; Toxoplasma gondii; Toxoplasmosis, Animal - parasitology; Toxoplasmosis, Animal - transmission; Transcription; Transcriptome; Vegetables; Veterinary medicine; Virulence - genetics
• ISSN: 1932-6203; 1932-6203
• DOI: 10.1371/journal.pone.0124473

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.