Comprehensive Evaluation of Toxoplasma gondii VEG and Neospora caninum LIV Genomes with Tachyzoite Stage Transcriptome and Proteome Defines Novel Transcript Features
Malas, Tareq Majed Yasin
Panigrahi, Aswini Kumar
Vermont, Sarah J.
Otto, Thomas D.
KAUST DepartmentBiological and Environmental Sciences and Engineering (BESE) Division
Bioscience Core Lab
Computer Science Program
Computer, Electrical and Mathematical Sciences and Engineering (CEMSE) Division
Pathogen Genomics Laboratory
Permanent link to this recordhttp://hdl.handle.net/10754/550412
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AbstractToxoplasma 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.
CitationRamaprasad 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
PublisherPublic Library of Science (PLoS)
PubMed Central IDPMC4395442
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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
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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