title: 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.
authors: Pathogen Genomics Laboratory, Biological and Environmental Sciences and Engineering (BESE) Division, King Abdullah University of Science and Technology (KAUST), Thuwal, Jeddah, Kingdom of Saudi Arabia.
authors: Abhinay
authors: A
authors: Ramaprasad
authors: Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark.
authors: Tobias
authors: T
authors: Mourier
authors: Pathogen Genomics Laboratory, Biological and Environmental Sciences and Engineering (BESE) Division, King Abdullah University of Science and Technology (KAUST), Thuwal, Jeddah, Kingdom of Saudi Arabia.
authors: Raeece
authors: R
authors: Naeem
authors: Pathogen Genomics Laboratory, Biological and Environmental Sciences and Engineering (BESE) Division, King Abdullah University of Science and Technology (KAUST), Thuwal, Jeddah, Kingdom of Saudi Arabia.
authors: Tareq B
authors: TB
authors: Malas
authors: Pathogen Genomics Laboratory, Biological and Environmental Sciences and Engineering (BESE) Division, King Abdullah University of Science and Technology (KAUST), Thuwal, Jeddah, Kingdom of Saudi Arabia.
authors: Ehab
authors: E
authors: Moussa
authors: Bioscience Core Laboratory (BCL), King Abdullah University of Science and Technology (KAUST), Thuwal, Jeddah, Kingdom of Saudi Arabia.
authors: Aswini
authors: A
authors: Panigrahi
authors: Institute of Infection and Global Health and School of Veterinary Science, Faculty of Health and Life Sciences, University of Liverpool, Liverpool, Merseyside, United Kingdom.
authors: Sarah J
authors: SJ
authors: Vermont
authors: Parasite Genomics Group, Wellcome Trust Sanger Institute (WTSI), Genome Campus, Hinxton, Cambridge, United Kingdom.
authors: Thomas D
authors: TD
authors: Otto
authors: Institute of Infection and Global Health and School of Veterinary Science, Faculty of Health and Life Sciences, University of Liverpool, Liverpool, Merseyside, United Kingdom.
authors: Jonathan
authors: J
authors: Wastling
authors: Pathogen Genomics Laboratory, Biological and Environmental Sciences and Engineering (BESE) Division, King Abdullah University of Science and Technology (KAUST), Thuwal, Jeddah, Kingdom of Saudi Arabia.
authors: Arnab
authors: A
authors: Pain
mesh_terms: D000818:Animals; D003048:Coccidiosis / Q000469:parasitology* / Q000635:transmission; D005786:Gene Expression Regulation; D018503:Genome, Protozoan; D023281:Genomics / Q000379:methods; D059014:High-Throughput Nucleotide Sequencing / Q000379:methods; D006790:Host-Parasite Interactions; D018445:Infectious Disease Transmission, Vertical; D018688:Neospora / Q000235:genetics* / Q000378:metabolism / Q000472:pathogenicity; D020543:Proteome / Q000032:analysis*; D062085:RNA, Long Noncoding / Q000235:genetics; D012045:Regulatory Sequences, Nucleic Acid / Q000235:genetics; D014122:Toxoplasma / Q000235:genetics* / Q000378:metabolism / Q000472:pathogenicity; D014124:Toxoplasmosis, Animal / Q000469:parasitology* / Q000635:transmission; D059467:Transcriptome; D014774:Virulence / Q000235:genetics
chemical_list: D020543:Proteome; D062085:RNA, Long Noncoding