ArticleBMC genomics2012
De novo reconstruction of the Toxoplasma gondii transcriptome improves on the current genome annotation and reveals alternatively spliced transcripts and putative long non-coding RNAs.
Article in BMC genomics, 2012. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 25 papers.
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Who cites it
25 citing papers in PubMed.
- The UTRs of Leishmania donovani vary in length and are enriched in potential regulatory structures.PLoS pathogens · 2026Article
- The UTRs of Leishmania donovani vary in length and are enriched in potential regulatory structures.bioRxiv : the preprint server for biology · 2025Article
- Full-Length Transcriptome Sequences Provide Insight Into Hermaphroditism of Freshwater Pearl MusselFrontiers in genetics · 2022Article
- Paving the Way: Contributions of Big Data to Apicomplexan and Kinetoplastid Research.Frontiers in cellular and infection microbiology · 2022Review
- Functional Intricacy and Symmetry of Long Non-Coding RNAs in Parasitic Infections.Frontiers in cellular and infection microbiology · 2021Review
- Latent Toxoplasmosis Effects on Rodents and Humans: How Much is Real and How Much is Media Hype?mBio · 2020Review
- Review
- Comparative studies of Toxoplasma gondii transcriptomes: insights into stage conversion based on gene expression profiling and alternative splicing.Parasites & vectors · 2018Article
- Comparative ribosome profiling uncovers a dominant role for translational control in Toxoplasma gondii.BMC genomics · 2017Article
- Characterization of the peripheral blood transcriptome and adaptive evolution of the MHC I and TLR gene families in the wolf (Canis lupus).BMC genomics · 2017Article
- The genome of the protozoan parasite Cystoisospora suis and a reverse vaccinology approach to identify vaccine candidates.International journal for parasitology · 2017Article
- Improved annotation with de novo transcriptome assembly in four social amoeba species.BMC genomics · 2017Article
- Identification and analysis of Eimeria nieschulzi gametocyte genes reveal splicing events of gam genes and conserved motifs in the wall-forming proteins within the genus Eimeria (Coccidia, Apicomplexa).Parasite (Paris, France) · 2017Article
- Integration of RNA-seq and proteomics data with genomics for improved genome annotation in Apicomplexan parasites.Proteomics · 2015Article
- A serine-arginine-rich (SR) splicing factor modulates alternative splicing of over a thousand genes in Toxoplasma gondii.Nucleic acids research · 2015Article
- Article
- Yeast three-hybrid screen identifies TgBRADIN/GRA24 as a negative regulator of Toxoplasma gondii bradyzoite differentiation.PloS one · 2015Article
- Incorporating alternative splicing and mRNA editing into the genetic analysis of complex traits.BioEssays : news and reviews in molecular, cellular and developmental biology · 2014Article
- Dual transcriptional profiling of mice and Toxoplasma gondii during acute and chronic infection.BMC genomics · 2014Article
- Transcript maturation in apicomplexan parasites.Current opinion in microbiology · 2014Review
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Authors and funding
5 authors.
Funding
Abstract
backgroundAccurate gene model predictions and annotation of alternative splicing events are imperative for genomic studies in organisms that contain genes with multiple exons. Currently most gene models for the intracellular parasite, Toxoplasma gondii, are based on computer model predictions without cDNA sequence verification. Additionally, the nature and extent of alternative splicing in Toxoplasma gondii is unknown. In this study, we used de novo transcript assembly and the published type II (ME49) genomic sequence to quantify the extent of alternative splicing in Toxoplasma and to improve the current Toxoplasma gene annotations.
resultsWe used high-throughput RNA-sequencing data to assemble full-length transcripts, independently of a reference genome, followed by gene annotation based on the ME49 genome. We assembled 13,533 transcripts overlapping with known ME49 genes in ToxoDB and then used this set to; a) improve the annotation in the untranslated regions of ToxoDB genes, b) identify novel exons within protein-coding ToxoDB genes, and c) report on 50 previously unidentified alternatively spliced transcripts. Additionally, we assembled a set of 2,930 transcripts not overlapping with any known ME49 genes in ToxoDB. From this set, we have identified 118 new ME49 genes, 18 novel Toxoplasma genes, and putative non-coding RNAs.
conclusionRNA-seq data and de novo transcript assembly provide a robust way to update incompletely annotated genomes, like the Toxoplasma genome. We have used RNA-seq to improve the annotation of several Toxoplasma genes, identify alternatively spliced genes, novel genes, novel exons, and putative non-coding RNAs.
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