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Breaking the 1000-gene barrier for Mimivirus using ultra-deep genome and transcriptome sequencing

BACKGROUND: Mimivirus, a giant dsDNA virus infecting Acanthamoeba, is the prototype of the mimiviridae family, the latest addition to the family of the nucleocytoplasmic large DNA viruses (NCLDVs). Its 1.2 Mb-genome was initially predicted to encode 917 genes. A subsequent RNA-Seq analysis precisely...

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Autores principales: Legendre, Matthieu, Santini, Sébastien, Rico, Alain, Abergel, Chantal, Claverie, Jean-Michel
Formato: Texto
Lenguaje:English
Publicado: BioMed Central 2011
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3058096/
https://www.ncbi.nlm.nih.gov/pubmed/21375749
http://dx.doi.org/10.1186/1743-422X-8-99
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author Legendre, Matthieu
Santini, Sébastien
Rico, Alain
Abergel, Chantal
Claverie, Jean-Michel
author_facet Legendre, Matthieu
Santini, Sébastien
Rico, Alain
Abergel, Chantal
Claverie, Jean-Michel
author_sort Legendre, Matthieu
collection PubMed
description BACKGROUND: Mimivirus, a giant dsDNA virus infecting Acanthamoeba, is the prototype of the mimiviridae family, the latest addition to the family of the nucleocytoplasmic large DNA viruses (NCLDVs). Its 1.2 Mb-genome was initially predicted to encode 917 genes. A subsequent RNA-Seq analysis precisely mapped many transcript boundaries and identified 75 new genes. FINDINGS: We now report a much deeper analysis using the SOLiD™ technology combining RNA-Seq of the Mimivirus transcriptome during the infectious cycle (202.4 Million reads), and a complete genome re-sequencing (45.3 Million reads). This study corrected the genome sequence and identified several single nucleotide polymorphisms. Our results also provided clear evidence of previously overlooked transcription units, including an important RNA polymerase subunit distantly related to Euryarchea homologues. The total Mimivirus gene count is now 1018, 11% greater than the original annotation. CONCLUSIONS: This study highlights the huge progress brought about by ultra-deep sequencing for the comprehensive annotation of virus genomes, opening the door to a complete one-nucleotide resolution level description of their transcriptional activity, and to the realistic modeling of the viral genome expression at the ultimate molecular level. This work also illustrates the need to go beyond bioinformatics-only approaches for the annotation of short protein and non-coding genes in viral genomes.
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spelling pubmed-30580962011-03-16 Breaking the 1000-gene barrier for Mimivirus using ultra-deep genome and transcriptome sequencing Legendre, Matthieu Santini, Sébastien Rico, Alain Abergel, Chantal Claverie, Jean-Michel Virol J Short Report BACKGROUND: Mimivirus, a giant dsDNA virus infecting Acanthamoeba, is the prototype of the mimiviridae family, the latest addition to the family of the nucleocytoplasmic large DNA viruses (NCLDVs). Its 1.2 Mb-genome was initially predicted to encode 917 genes. A subsequent RNA-Seq analysis precisely mapped many transcript boundaries and identified 75 new genes. FINDINGS: We now report a much deeper analysis using the SOLiD™ technology combining RNA-Seq of the Mimivirus transcriptome during the infectious cycle (202.4 Million reads), and a complete genome re-sequencing (45.3 Million reads). This study corrected the genome sequence and identified several single nucleotide polymorphisms. Our results also provided clear evidence of previously overlooked transcription units, including an important RNA polymerase subunit distantly related to Euryarchea homologues. The total Mimivirus gene count is now 1018, 11% greater than the original annotation. CONCLUSIONS: This study highlights the huge progress brought about by ultra-deep sequencing for the comprehensive annotation of virus genomes, opening the door to a complete one-nucleotide resolution level description of their transcriptional activity, and to the realistic modeling of the viral genome expression at the ultimate molecular level. This work also illustrates the need to go beyond bioinformatics-only approaches for the annotation of short protein and non-coding genes in viral genomes. BioMed Central 2011-03-04 /pmc/articles/PMC3058096/ /pubmed/21375749 http://dx.doi.org/10.1186/1743-422X-8-99 Text en Copyright ©2011 Legendre et al; licensee BioMed Central Ltd. http://creativecommons.org/licenses/by/2.0 This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.
spellingShingle Short Report
Legendre, Matthieu
Santini, Sébastien
Rico, Alain
Abergel, Chantal
Claverie, Jean-Michel
Breaking the 1000-gene barrier for Mimivirus using ultra-deep genome and transcriptome sequencing
title Breaking the 1000-gene barrier for Mimivirus using ultra-deep genome and transcriptome sequencing
title_full Breaking the 1000-gene barrier for Mimivirus using ultra-deep genome and transcriptome sequencing
title_fullStr Breaking the 1000-gene barrier for Mimivirus using ultra-deep genome and transcriptome sequencing
title_full_unstemmed Breaking the 1000-gene barrier for Mimivirus using ultra-deep genome and transcriptome sequencing
title_short Breaking the 1000-gene barrier for Mimivirus using ultra-deep genome and transcriptome sequencing
title_sort breaking the 1000-gene barrier for mimivirus using ultra-deep genome and transcriptome sequencing
topic Short Report
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3058096/
https://www.ncbi.nlm.nih.gov/pubmed/21375749
http://dx.doi.org/10.1186/1743-422X-8-99
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