Viruses have been recognized as the most abundant and diversified component of aquatic environments. The development of metagenomic approaches, indeed, has provided an unprecedented level of access to viral genomes from different environments, making it possible to characterize their taxonomic and functional diversity. Despite this, viral diversity in benthic deep--sea ecosystems is still completely unknown. Multiple bioinformatic tools were leveraged to analyze viral sequences in environmental samples and evaluate performance in virome analyses. In this study we compared three metagenomic sequence annotation pipelines (MG--RAST, VMGAP, MetaVir) to test their efficiency in the analysis of viromes from different deep--sea sediment samples. MetaVir identified a higher number of viral strains compared to MG--RAST and VMGAP (80% vs.45--55%, respectively) and a different pattern of assemblage composition. Instead, contrary to MetaVir, MG--RAST and VMGAP allowed the identification of putative proteins and functions providing important information on the hypothetical metabolic role of the viromes analysed. This study indicates that the integration of information from different bioinformatic tools can help to shed light on the enormous genetic diversity contained in viruses inhabiting the largest ecosystem of Earth.
Does viral diversity assessment in deep-sea sediments depend on the selection of bioinformatic tools? / Riccioni G.; Dell’Anno A.; Zeigler Allen L.; Tangherlini M.; Corinaldesi C.. - ELETTRONICO. - (2013), pp. 64-64. (Intervento presentato al convegno XXIII congress SitE- Società Italiana di Ecologia, “Ecology for a sustainable blue and green growth” tenutosi a Ancona nel 16-18 Settembre 2013).
Does viral diversity assessment in deep-sea sediments depend on the selection of bioinformatic tools?
RICCIONI, GIULIA;
2013
Abstract
Viruses have been recognized as the most abundant and diversified component of aquatic environments. The development of metagenomic approaches, indeed, has provided an unprecedented level of access to viral genomes from different environments, making it possible to characterize their taxonomic and functional diversity. Despite this, viral diversity in benthic deep--sea ecosystems is still completely unknown. Multiple bioinformatic tools were leveraged to analyze viral sequences in environmental samples and evaluate performance in virome analyses. In this study we compared three metagenomic sequence annotation pipelines (MG--RAST, VMGAP, MetaVir) to test their efficiency in the analysis of viromes from different deep--sea sediment samples. MetaVir identified a higher number of viral strains compared to MG--RAST and VMGAP (80% vs.45--55%, respectively) and a different pattern of assemblage composition. Instead, contrary to MetaVir, MG--RAST and VMGAP allowed the identification of putative proteins and functions providing important information on the hypothetical metabolic role of the viromes analysed. This study indicates that the integration of information from different bioinformatic tools can help to shed light on the enormous genetic diversity contained in viruses inhabiting the largest ecosystem of Earth.I documenti in IRIS sono protetti da copyright e tutti i diritti sono riservati, salvo diversa indicazione.
