New assembly, reannotation and analysis of the Entamoeba histolytica genome reveal new genomic features and protein content information.
In order to maintain genome information accurately and relevantly, original genome annotations need to be updated and evaluated regularly. Manual reannotation of genomes is important as it can significantly reduce the propagation of errors and consequently diminishes the time spent on mistaken resea...
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ftdoajarticles:oai:doaj.org/article:7a63ab065e1a4aea96f33f13e6d6e192 2023-05-15T15:12:37+02:00 New assembly, reannotation and analysis of the Entamoeba histolytica genome reveal new genomic features and protein content information. Hernan A Lorenzi Daniela Puiu Jason R Miller Lauren M Brinkac Paolo Amedeo Neil Hall Elisabet V Caler 2010-06-01T00:00:00Z https://doi.org/10.1371/journal.pntd.0000716 https://doaj.org/article/7a63ab065e1a4aea96f33f13e6d6e192 EN eng Public Library of Science (PLoS) http://europepmc.org/articles/PMC2886108?pdf=render https://doaj.org/toc/1935-2727 https://doaj.org/toc/1935-2735 1935-2727 1935-2735 doi:10.1371/journal.pntd.0000716 https://doaj.org/article/7a63ab065e1a4aea96f33f13e6d6e192 PLoS Neglected Tropical Diseases, Vol 4, Iss 6, p e716 (2010) Arctic medicine. Tropical medicine RC955-962 Public aspects of medicine RA1-1270 article 2010 ftdoajarticles https://doi.org/10.1371/journal.pntd.0000716 2022-12-30T21:59:59Z In order to maintain genome information accurately and relevantly, original genome annotations need to be updated and evaluated regularly. Manual reannotation of genomes is important as it can significantly reduce the propagation of errors and consequently diminishes the time spent on mistaken research. For this reason, after five years from the initial submission of the Entamoeba histolytica draft genome publication, we have re-examined the original 23 Mb assembly and the annotation of the predicted genes.The evaluation of the genomic sequence led to the identification of more than one hundred artifactual tandem duplications that were eliminated by re-assembling the genome. The reannotation was done using a combination of manual and automated genome analysis. The new 20 Mb assembly contains 1,496 scaffolds and 8,201 predicted genes, of which 60% are identical to the initial annotation and the remaining 40% underwent structural changes. Functional classification of 60% of the genes was modified based on recent sequence comparisons and new experimental data. We have assigned putative function to 3,788 proteins (46% of the predicted proteome) based on the annotation of predicted gene families, and have identified 58 protein families of five or more members that share no homology with known proteins and thus could be entamoeba specific. Genome analysis also revealed new features such as the presence of segmental duplications of up to 16 kb flanked by inverted repeats, and the tight association of some gene families with transposable elements.This new genome annotation and analysis represents a more refined and accurate blueprint of the pathogen genome, and provides an upgraded tool as reference for the study of many important aspects of E. histolytica biology, such as genome evolution and pathogenesis. Article in Journal/Newspaper Arctic Directory of Open Access Journals: DOAJ Articles Arctic PLoS Neglected Tropical Diseases 4 6 e716 |
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Directory of Open Access Journals: DOAJ Articles |
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ftdoajarticles |
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English |
topic |
Arctic medicine. Tropical medicine RC955-962 Public aspects of medicine RA1-1270 |
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Arctic medicine. Tropical medicine RC955-962 Public aspects of medicine RA1-1270 Hernan A Lorenzi Daniela Puiu Jason R Miller Lauren M Brinkac Paolo Amedeo Neil Hall Elisabet V Caler New assembly, reannotation and analysis of the Entamoeba histolytica genome reveal new genomic features and protein content information. |
topic_facet |
Arctic medicine. Tropical medicine RC955-962 Public aspects of medicine RA1-1270 |
description |
In order to maintain genome information accurately and relevantly, original genome annotations need to be updated and evaluated regularly. Manual reannotation of genomes is important as it can significantly reduce the propagation of errors and consequently diminishes the time spent on mistaken research. For this reason, after five years from the initial submission of the Entamoeba histolytica draft genome publication, we have re-examined the original 23 Mb assembly and the annotation of the predicted genes.The evaluation of the genomic sequence led to the identification of more than one hundred artifactual tandem duplications that were eliminated by re-assembling the genome. The reannotation was done using a combination of manual and automated genome analysis. The new 20 Mb assembly contains 1,496 scaffolds and 8,201 predicted genes, of which 60% are identical to the initial annotation and the remaining 40% underwent structural changes. Functional classification of 60% of the genes was modified based on recent sequence comparisons and new experimental data. We have assigned putative function to 3,788 proteins (46% of the predicted proteome) based on the annotation of predicted gene families, and have identified 58 protein families of five or more members that share no homology with known proteins and thus could be entamoeba specific. Genome analysis also revealed new features such as the presence of segmental duplications of up to 16 kb flanked by inverted repeats, and the tight association of some gene families with transposable elements.This new genome annotation and analysis represents a more refined and accurate blueprint of the pathogen genome, and provides an upgraded tool as reference for the study of many important aspects of E. histolytica biology, such as genome evolution and pathogenesis. |
format |
Article in Journal/Newspaper |
author |
Hernan A Lorenzi Daniela Puiu Jason R Miller Lauren M Brinkac Paolo Amedeo Neil Hall Elisabet V Caler |
author_facet |
Hernan A Lorenzi Daniela Puiu Jason R Miller Lauren M Brinkac Paolo Amedeo Neil Hall Elisabet V Caler |
author_sort |
Hernan A Lorenzi |
title |
New assembly, reannotation and analysis of the Entamoeba histolytica genome reveal new genomic features and protein content information. |
title_short |
New assembly, reannotation and analysis of the Entamoeba histolytica genome reveal new genomic features and protein content information. |
title_full |
New assembly, reannotation and analysis of the Entamoeba histolytica genome reveal new genomic features and protein content information. |
title_fullStr |
New assembly, reannotation and analysis of the Entamoeba histolytica genome reveal new genomic features and protein content information. |
title_full_unstemmed |
New assembly, reannotation and analysis of the Entamoeba histolytica genome reveal new genomic features and protein content information. |
title_sort |
new assembly, reannotation and analysis of the entamoeba histolytica genome reveal new genomic features and protein content information. |
publisher |
Public Library of Science (PLoS) |
publishDate |
2010 |
url |
https://doi.org/10.1371/journal.pntd.0000716 https://doaj.org/article/7a63ab065e1a4aea96f33f13e6d6e192 |
geographic |
Arctic |
geographic_facet |
Arctic |
genre |
Arctic |
genre_facet |
Arctic |
op_source |
PLoS Neglected Tropical Diseases, Vol 4, Iss 6, p e716 (2010) |
op_relation |
http://europepmc.org/articles/PMC2886108?pdf=render https://doaj.org/toc/1935-2727 https://doaj.org/toc/1935-2735 1935-2727 1935-2735 doi:10.1371/journal.pntd.0000716 https://doaj.org/article/7a63ab065e1a4aea96f33f13e6d6e192 |
op_doi |
https://doi.org/10.1371/journal.pntd.0000716 |
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PLoS Neglected Tropical Diseases |
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4 |
container_issue |
6 |
container_start_page |
e716 |
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