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A large-scale proteogenomics study of apicomplexan pathogens—Toxoplasma gondii and Neospora caninum
Proteomics data can supplement genome annotation efforts, for example being used to confirm gene models or correct gene annotation errors. Here, we present a large-scale proteogenomics study of two important apicomplexan pathogens: Toxoplasma gondii and Neospora caninum. We queried proteomics data a...
Autores principales: | , , , , , , , , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
Blackwell Publishing Ltd
2015
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4692086/ https://www.ncbi.nlm.nih.gov/pubmed/25867681 http://dx.doi.org/10.1002/pmic.201400553 |
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author | Krishna, Ritesh Xia, Dong Sanderson, Sanya Shanmugasundram, Achchuthan Vermont, Sarah Bernal, Axel Daniel-Naguib, Gianluca Ghali, Fawaz Brunk, Brian P Roos, David S Wastling, Jonathan M Jones, Andrew R |
author_facet | Krishna, Ritesh Xia, Dong Sanderson, Sanya Shanmugasundram, Achchuthan Vermont, Sarah Bernal, Axel Daniel-Naguib, Gianluca Ghali, Fawaz Brunk, Brian P Roos, David S Wastling, Jonathan M Jones, Andrew R |
author_sort | Krishna, Ritesh |
collection | PubMed |
description | Proteomics data can supplement genome annotation efforts, for example being used to confirm gene models or correct gene annotation errors. Here, we present a large-scale proteogenomics study of two important apicomplexan pathogens: Toxoplasma gondii and Neospora caninum. We queried proteomics data against a panel of official and alternate gene models generated directly from RNASeq data, using several newly generated and some previously published MS datasets for this meta-analysis. We identified a total of 201 996 and 39 953 peptide-spectrum matches for T. gondii and N. caninum, respectively, at a 1% peptide FDR threshold. This equated to the identification of 30 494 distinct peptide sequences and 2921 proteins (matches to official gene models) for T. gondii, and 8911 peptides/1273 proteins for N. caninum following stringent protein-level thresholding. We have also identified 289 and 140 loci for T. gondii and N. caninum, respectively, which mapped to RNA-Seq-derived gene models used in our analysis and apparently absent from the official annotation (release 10 from EuPathDB) of these species. We present several examples in our study where the RNA-Seq evidence can help in correction of the current gene model and can help in discovery of potential new genes. The findings of this study have been integrated into the EuPathDB. The data have been deposited to the ProteomeXchange with identifiers PXD000297and PXD000298. |
format | Online Article Text |
id | pubmed-4692086 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2015 |
publisher | Blackwell Publishing Ltd |
record_format | MEDLINE/PubMed |
spelling | pubmed-46920862016-01-04 A large-scale proteogenomics study of apicomplexan pathogens—Toxoplasma gondii and Neospora caninum Krishna, Ritesh Xia, Dong Sanderson, Sanya Shanmugasundram, Achchuthan Vermont, Sarah Bernal, Axel Daniel-Naguib, Gianluca Ghali, Fawaz Brunk, Brian P Roos, David S Wastling, Jonathan M Jones, Andrew R Proteomics Microbiology Proteomics data can supplement genome annotation efforts, for example being used to confirm gene models or correct gene annotation errors. Here, we present a large-scale proteogenomics study of two important apicomplexan pathogens: Toxoplasma gondii and Neospora caninum. We queried proteomics data against a panel of official and alternate gene models generated directly from RNASeq data, using several newly generated and some previously published MS datasets for this meta-analysis. We identified a total of 201 996 and 39 953 peptide-spectrum matches for T. gondii and N. caninum, respectively, at a 1% peptide FDR threshold. This equated to the identification of 30 494 distinct peptide sequences and 2921 proteins (matches to official gene models) for T. gondii, and 8911 peptides/1273 proteins for N. caninum following stringent protein-level thresholding. We have also identified 289 and 140 loci for T. gondii and N. caninum, respectively, which mapped to RNA-Seq-derived gene models used in our analysis and apparently absent from the official annotation (release 10 from EuPathDB) of these species. We present several examples in our study where the RNA-Seq evidence can help in correction of the current gene model and can help in discovery of potential new genes. The findings of this study have been integrated into the EuPathDB. The data have been deposited to the ProteomeXchange with identifiers PXD000297and PXD000298. Blackwell Publishing Ltd 2015-08 2015-05-15 /pmc/articles/PMC4692086/ /pubmed/25867681 http://dx.doi.org/10.1002/pmic.201400553 Text en © 2015 The Authors. PROTEOMICS published by Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim. http://creativecommons.org/licenses/by/4.0/ This is an open access article under the terms of the Creative Commons Attribution License, which permits use, distribution and reproduction in any medium, provided the original work is properly cited. |
spellingShingle | Microbiology Krishna, Ritesh Xia, Dong Sanderson, Sanya Shanmugasundram, Achchuthan Vermont, Sarah Bernal, Axel Daniel-Naguib, Gianluca Ghali, Fawaz Brunk, Brian P Roos, David S Wastling, Jonathan M Jones, Andrew R A large-scale proteogenomics study of apicomplexan pathogens—Toxoplasma gondii and Neospora caninum |
title | A large-scale proteogenomics study of apicomplexan pathogens—Toxoplasma gondii and Neospora caninum |
title_full | A large-scale proteogenomics study of apicomplexan pathogens—Toxoplasma gondii and Neospora caninum |
title_fullStr | A large-scale proteogenomics study of apicomplexan pathogens—Toxoplasma gondii and Neospora caninum |
title_full_unstemmed | A large-scale proteogenomics study of apicomplexan pathogens—Toxoplasma gondii and Neospora caninum |
title_short | A large-scale proteogenomics study of apicomplexan pathogens—Toxoplasma gondii and Neospora caninum |
title_sort | large-scale proteogenomics study of apicomplexan pathogens—toxoplasma gondii and neospora caninum |
topic | Microbiology |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4692086/ https://www.ncbi.nlm.nih.gov/pubmed/25867681 http://dx.doi.org/10.1002/pmic.201400553 |
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