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HoloVir: A Workflow for Investigating the Diversity and Function of Viruses in Invertebrate Holobionts.

Authors :
Laffy PW
Wood-Charlson EM
Turaev D
Weynberg KD
Botté ES
van Oppen MJ
Webster NS
Rattei T
Source :
Frontiers in microbiology [Front Microbiol] 2016 Jun 09; Vol. 7, pp. 822. Date of Electronic Publication: 2016 Jun 09 (Print Publication: 2016).
Publication Year :
2016

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.

Details

Language :
English
ISSN :
1664-302X
Volume :
7
Database :
MEDLINE
Journal :
Frontiers in microbiology
Publication Type :
Academic Journal
Accession number :
27375564
Full Text :
https://doi.org/10.3389/fmicb.2016.00822