Comprehensive Evaluation of Toxoplasma gondii VEG and Neospora caninum LIV Genomes with Tachyzoite Stage Transcriptome and Proteome Defines Novel Transcript Features

Handle URI:
http://hdl.handle.net/10754/550412
Title:
Comprehensive Evaluation of Toxoplasma gondii VEG and Neospora caninum LIV Genomes with Tachyzoite Stage Transcriptome and Proteome Defines Novel Transcript Features
Authors:
Ramaprasad, Abhinay ( 0000-0001-9372-5526 ) ; Mourier, Tobias; Naeem, Raeece ( 0000-0003-1734-1007 ) ; Malas, Tareq B.; Moussa, Ehab; Panigrahi, Aswini; Vermont, Sarah J.; Otto, Thomas D.; Wastling, Jonathan; Pain, Arnab ( 0000-0002-1755-2819 )
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.
KAUST Department:
Pathogen Genomics Laboratory; Biological and Environmental Sciences and Engineering (BESE) Division; Biosciences Core Lab
Citation:
Ramaprasad 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
Publisher:
Public Library of Science
Journal:
PLOS ONE
Issue Date:
13-Apr-2015
DOI:
10.1371/journal.pone.0124473
PubMed ID:
25875305
PubMed Central ID:
PMC4395442
Type:
Article
ISSN:
1932-6203
Additional Links:
http://dx.plos.org/10.1371/journal.pone.0124473
Appears in Collections:
Articles; Biosciences Core Lab; Biological and Environmental Sciences and Engineering (BESE) Division

Full metadata record

DC FieldValue Language
dc.contributor.authorRamaprasad, Abhinayen
dc.contributor.authorMourier, Tobiasen
dc.contributor.authorNaeem, Raeeceen
dc.contributor.authorMalas, Tareq B.en
dc.contributor.authorMoussa, Ehaben
dc.contributor.authorPanigrahi, Aswinien
dc.contributor.authorVermont, Sarah J.en
dc.contributor.authorOtto, Thomas D.en
dc.contributor.authorWastling, Jonathanen
dc.contributor.authorPain, Arnaben
dc.date.accessioned2015-04-21T14:12:37Zen
dc.date.available2015-04-21T14:12:37Zen
dc.date.issued2015-04-13en
dc.identifier.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.0124473en
dc.identifier.issn1932-6203en
dc.identifier.pmid25875305en
dc.identifier.doi10.1371/journal.pone.0124473en
dc.identifier.urihttp://hdl.handle.net/10754/550412en
dc.description.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.en
dc.publisherPublic Library of Scienceen
dc.relation.urlhttp://dx.plos.org/10.1371/journal.pone.0124473en
dc.rightsThis is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are crediteden
dc.titleComprehensive Evaluation of Toxoplasma gondii VEG and Neospora caninum LIV Genomes with Tachyzoite Stage Transcriptome and Proteome Defines Novel Transcript Featuresen
dc.typeArticleen
dc.contributor.departmentPathogen Genomics Laboratoryen
dc.contributor.departmentBiological and Environmental Sciences and Engineering (BESE) Divisionen
dc.contributor.departmentBiosciences Core Laben
dc.identifier.journalPLOS ONEen
dc.identifier.pmcidPMC4395442en
dc.eprint.versionPublisher's Version/PDFen
dc.contributor.institutionCentre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmarken
dc.contributor.institutionInstitute of Infection and Global Health and School of Veterinary Science, Faculty of Health and Life Sciences, University of Liverpool, Liverpool, Merseyside, United Kingdomen
dc.contributor.institutionParasite Genomics Group, Wellcome Trust Sanger Institute (WTSI), Genome Campus, Hinxton, Cambridge, United Kingdomen
kaust.authorRamaprasad, Abhinayen
kaust.authorNaeem, Raeeceen
kaust.authorMalas, Tareq Majed Yasinen
kaust.authorMoussa, Ehaben
kaust.authorPanigrahi, Aswini Kumaren
kaust.authorPain, Arnaben

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