title: HoloVir: A Workflow for Investigating the Diversity and Function of Viruses in Invertebrate Holobionts.
abstract: Abundant bioinformatics resources are available for the study of complex microbial metagenomes, however their utility in viral metagenomics is limited. 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. 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 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. 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. 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.
authors.affiliation: Australian Institute of Marine Science Townsville, QLD, Australia.
authors.forename: Patrick W
authors.initials: PW
authors.lastname: Laffy
authors.affiliation: Center for Microbial Oceanography: Research and Education, University of Hawai'i at Mānoa Honolulu, HI, USA.
authors.forename: Elisha M
authors.initials: EM
authors.lastname: Wood-Charlson
authors.affiliation: Division of Computational Systems Biology, Department of Microbiology and Ecosystem Science, University of Vienna Vienna, Austria.
authors.forename: Dmitrij
authors.initials: D
authors.lastname: Turaev
authors.affiliation: Australian Institute of Marine Science Townsville, QLD, Australia.
authors.forename: Karen D
authors.initials: KD
authors.lastname: Weynberg
authors.affiliation: Australian Institute of Marine Science Townsville, QLD, Australia.
authors.forename: Emmanuelle S
authors.initials: ES
authors.lastname: Botté
authors.affiliation: Australian Institute of Marine ScienceTownsville, QLD, Australia; School of Biosciences, University of MelbourneMelbourne, VIC, Australia.
authors.forename: Madeleine J H
authors.initials: MJ
authors.lastname: van Oppen
authors.affiliation: Australian Institute of Marine Science Townsville, QLD, Australia.
authors.forename: Nicole S
authors.initials: NS
authors.lastname: Webster
authors.affiliation: Division of Computational Systems Biology, Department of Microbiology and Ecosystem Science, University of Vienna Vienna, Austria.
authors.forename: Thomas
authors.initials: T
authors.lastname: Rattei
keywords: Bioinformatics tools; host-associated communities; marine ecology; marine invertebrates; symbiosis; viral metagenomics