Horizontal gene transfer and metabolic reprogramming by viral-encoded auxiliary metabolic genes is another important ecosystem role ( Jiang and Paul, 1998 Hurwitz et al., 2015) with the recombination of viral and host genes during infection often triggering changes in host metabolism, immunity, distribution and evolution ( Rohwer and Thurber, 2009) as well as shaping viral genomes ( Lindell et al., 2007).
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This viral-induced mortality can be selective, thereby determining host community composition and acting as an important bottom-up ecological driver in marine ecosystems ( Bouvier and del Giorgio, 2007 Hewson and Fuhrman, 2007). However, despite these limitations, research over the past decade has shown that viruses play a vital role in biogeochemical cycles as they modulate microbially-driven processes through mortality and subsequent release of organic matter and inorganic nutrients that become available for other microorganisms to consume ( Suttle, 2005 Weitz and Wilhelm, 2012). For instance, viruses can contribute to host survival by suspending unnecessary metabolic activities during unfavorable environmental conditions, while they modulate host metabolic gene expression ( Paul, 2008) and confer host fitness ( Roossinck, 2011).ĭue to limitations in traditional methodologies used for studying complex viral populations, including a lack of suitable marker genes, and limited methods designed specifically for viruses, our understanding about the specific roles viruses play in marine ecosystems has lagged behind our knowledge of the functional roles of cellular microorganisms. However, viruses are not exclusively agents of mortality, and in some cases, they can form mutually beneficial partnerships with their hosts ( Weinbauer and Rassoulzadegan, 2004). Viruses infect all living bacterial, archaeal and eukaryotic cells ( Fuhrman, 1999 Wommack and Colwell, 2000 Danovaro et al., 2008 Rohwer and Thurber, 2009) and are responsible for high turnover rates of their microbial hosts and subsequent nutrient cycling in the world's oceans ( Weitz and Wilhelm, 2012). Marine viruses are the most abundant biological entities in the oceans, often exceeding the number of bacteria 10-fold ( Wommack and Colwell, 2000 Suttle, 2005, 2007) and having high local and global diversity ( Brum et al., 2015). Application of HoloVir to viral metagenomes from the coral Pocillopora damicornis and the sponge Rhopaloeides odorabile demonstrated that HoloVir provides a valuable tool to characterize holobiont viral communities across species, environments, or experiments. Broad functional classification of the predicted genes is provided by assignment of COG microbial functional category classifications using EggNOG and higher resolution functional analysis is achieved by searching for enrichment of specific Swiss-Prot keywords within the viral metagenome. HoloVir performs pairwise comparisons of single read and predicted gene datasets against the viral RefSeq database to assign taxonomy and additional comparison to phage-specific and cellular markers is undertaken to support the taxonomic assignments and identify potential cellular contamination. Simulated viral metagenomes comprising varying levels of viral diversity and abundance were used to determine the optimal assembly and gene prediction strategy, and multiple sequence assembly methods and gene prediction tools were tested in order to optimize our analysis workflow. HoloVir is a robust and flexible data analysis pipeline that provides an optimized and validated workflow for taxonomic and functional characterization of viral metagenomes derived from invertebrate holobionts. 4School of Biosciences, University of Melbourne, Melbourne, VIC, AustraliaĪbundant bioinformatics resources are available for the study of complex microbial metagenomes, however their utility in viral metagenomics is limited.3Division of Computational Systems Biology, Department of Microbiology and Ecosystem Science, University of Vienna, Vienna, Austria.2Center for Microbial Oceanography: Research and Education, University of Hawai‘i at Mānoa, Honolulu, HI, USA.
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