ERP008859 PRJEB7873 ena-STUDY-KAUST-27-11-2014-10:24:28:422-2110 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. 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. Automated gene prediction tools that were used for gene annotation can lead to inaccurate gene models and lack information on untranslated regions and non-coding transcripts. Here, we describe a manual re-annotation of these genomes based on strand-specific RNA sequencing and shotgun proteomics. We have corrected the structures of over one third of the gene models and have annotated the complete set of untranslated regions (UTRs). We observe distinctly long UTRs in both the ?organisms??, almost four times longer than other eukaryotes?. We have also identified a putative set of cis-natural antisense transcripts (cis-NATs) and long intergenic non-coding RNAs (lincRNAs). With these, we have significantly improved the quality of annotation in the genomes to serve as a manually curated base for future research on these organisms. Strand-specific RNA-sequencing and manual re-annotation of Toxoplasma gondii VEG and Neospora caninum LIV genomes 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. Automated gene prediction tools that were used for gene annotation can lead to inaccurate gene models and lack information on untranslated regions and non-coding transcripts. Here, we describe a manual re-annotation of these genomes based on strand-specific RNA sequencing and shotgun proteomics. We have corrected the structures of over one third of the gene models and have annotated the complete set of untranslated regions (UTRs). We observe distinctly long UTRs in both the ?organisms??, almost four times longer than other eukaryotes?. We have also identified a putative set of cis-natural antisense transcripts (cis-NATs) and long intergenic non-coding RNAs (lincRNAs). With these, we have significantly improved the quality of annotation in the genomes to serve as a manually curated base for future research on these organisms.