Breaking the 1000-gene barrier for Mimivirus using ultra-deep genome and transcriptome sequencing - PubMed (original) (raw)

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

Matthieu Legendre et al. Virol J. 2011.

Abstract

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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Figures

Figure 1

Flow chart of the Mimivirus genome correction pipeline. The upper panel illustrates the correction procedure and the lower panel the annotation method. Colors are used for clarity: datasets are in purple, genomes are in green, sequence manipulations (mapping, duplicate removal, or modifications) are in yellow, computation steps are in blue and genes in red. The upper left graph represents the decrease in substitutions (in red) and indels (in black) identified during the iterative genome correction process, together with the increase in the total number of reads (in green) mapped to genome.

Figure 2

Discovery of a component of the Mimivirus transcription apparatus. A) Mimivirus genome browser (URL:

http://www.igs.cnrs-mrs.fr/mimivirus/

) screenshot showing the newly discovered component of the transcription apparatus (R357b) in its genomic context. Three informative tracks are displayed: the protein coding genes, the late gene expression signals, and the gene expression data from the SOLiD™ RNA-seq experiment. Transcriptome data is shown at each genomic position (for each of the 9 samples) going from white (not expressed) to red (highly expressed) in the forward strand, and white to blue (highly expressed) in the reverse strand. B) Protein sequence alignment of the Mimivirus R357b gene and the most similar homologous sequences from the giant virus CroV and the two archea Methanocella paludicola and Ferroplasma acidarmanus.

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Breaking the 1000-gene barrier for Mimivirus using ultra-deep genome and transcriptome sequencing - PubMed (original) (raw)