About: Characterisation of the faecal virome of captive and wild Tasmanian devils using virus-like particles metagenomics and meta-transcriptomics

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About: Characterisation of the faecal virome of captive and wild Tasmanian devils using virus-like particles metagenomics and meta-transcriptomics Goto Sponge NotDistinct Permalink

An Entity of Type : schema:ScholarlyArticle, within Data Space : wasabi.inria.fr associated with source document(s)

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type	Academic Article research paper schema:ScholarlyArticle
isDefinedBy	Covid-on-the-Web dataset
title	Characterisation of the faecal virome of captive and wild Tasmanian devils using virus-like particles metagenomics and meta-transcriptomics
source	BioRxiv; MedRxiv
abstract	The Tasmanian devil is an endangered carnivorous marsupial threatened by devil facial tumour disease (DFTD). While research on DFTD has been extensive, little is known about the viruses present in devils, and whether any of these are of potential conservation relevance for this endangered species. Using both metagenomics based on virus-like particle (VLP) enrichment and sequence-independent amplification (VLP metagenomics), and meta-transcriptomics based on bulk RNA sequencing, we characterised and compared the faecal viromes of captive and wild Tasmanian devils. A total of 54 devil faecal samples collected from captive (n = 2) and wild (n = 4) populations were processed for virome characterisation using both approaches. We detected many novel, highly divergent viruses, including vertebrate viruses, bacteriophage and other dietary associated plant and insect viruses. In total, 18 new vertebrate viruses, including novel sapelovirus, astroviruses, bocaviruses, papillomaviruses and gammaherpesvirus were identified, as well as known mammalian pathogens including rabbit haemorrhagic disease virus 2 (RHDV2). Captive devils showed significantly lower levels of viral diversity than wild devils. Comparison of the two methodological approaches revealed substantial differences in the number and types of viruses detected, with meta-transcriptomics mainly identifying RNA viruses, and VLP metagenomics largely identifying DNA viruses. This study has greatly expanded our knowledge of eukaryotic viruses in the Tasmanian devil and provides important baseline information that will contribute to the conservation and captive management of this endangered species. In addition, our results showed that a combination of VLP metagenomics and meta-transcriptomics may be a more comprehensive approach to virome characterisation than either method alone.
has issue date	2018-10-15(xsd:dateTime)
bibo:doi	10.1101/443457
has license	medrxiv
sha1sum (hex)	564f8823050b52b5f5c36638ac1ae07557963f36
schema:url	https://doi.org/10.1101/443457
resource representing a document's title	Characterisation of the faecal virome of captive and wild Tasmanian devils using virus-like particles metagenomics and meta-transcriptomics
schema:publication	bioRxiv
resource representing a document's body	covid:564f8823050b52b5f5c36638ac1ae07557963f36#body_text
is schema:about of	named entity 'virome' named entity 'captive populations' named entity 'peer-reviewed' named entity 'kangaroos' named entity 'carnivorous marsupial' named entity 'metagenomics' named entity 'Bettongia penicillata' named entity 'preprint' named entity 'preprint' named entity 'peer-reviewed' named entity 'peer-reviewed' named entity 'Tasmanian devil' named entity 'scavenger' named entity 'Tasmanian devil' named entity 'preprint' named entity 'bioRxiv' named entity 'preprint' named entity 'protein' named entity 'bioRxiv' named entity 'peer-reviewed' named entity 'possums' named entity 'peer-reviewed' named entity 'Australia' named entity 'fruit' named entity 'peer-reviewed' named entity 'preprint' named entity 'bioRxiv' named entity 'Listed as endangered' named entity 'mtDNA' named entity 'preprint' named entity 'peer-reviewed' named entity 'metagenomics' named entity 'preprint' named entity 'carrion' named entity 'preprint' named entity '1, 2' named entity 'preprint' named entity 'DFTD' named entity 'threat of extinction' named entity 'wallabies' named entity 'preprint' named entity 'protein' named entity 'preprint' named entity 'doi' named entity 'DFTD' named entity 'devil facial tumour disease' named entity 'doi' named entity 'preprint' named entity 'peer-reviewed' named entity 'preprint' named entity 'Tasmania' named entity 'mammals' named entity 'meta-transcriptomics' named entity 'transcriptome' named entity 'Sarcophilus harrisii' named entity 'preprint' named entity 'DNA helicase' named entity 'peer-reviewed' named entity 'liver' named entity 'alpha diversity' named entity 'viruses' named entity 'meta-transcriptomics' named entity 'bioRxiv' named entity 'meta-transcriptomics' named entity 'preprint' named entity 'preprint' named entity 'bacteriophage' named entity 'Phylogenetic' named entity 'Phylogenetic analysis' named entity 'viruses' named entity 'meta-transcriptomics' named entity 'peer-reviewed' named entity 'viral replication' named entity 'peer-reviewed' named entity 'preprint' named entity 'hybridization' named entity 'virome' named entity 'Characterisation' named entity 'faecal' named entity 'Tasmanian'
is part of of	Characterisation of the faecal virome of captive and wild Tasmanian devils using virus-like particles metagenomics and meta-transcriptomics covid:564f8823050b52b5f5c36638ac1ae07557963f36#body_text The Tasmanian devil is an endangered carnivorous marsupial threatened by devil facial tumour disease (DFTD). While research on DFTD has been extensive, little is known about the viruses present in devils, and whether any of these are of potential conservation relevance for this endangered species. Using both metagenomics based on virus-like particle (VLP) enrichment and sequence-independent amplification (VLP metagenomics), and meta-transcriptomics based on bulk RNA sequencing, we characterised and compared the faecal viromes of captive and wild Tasmanian devils. A total of 54 devil faecal samples collected from captive (n = 2) and wild (n = 4) populations were processed for virome characterisation using both approaches. We detected many novel, highly divergent viruses, including vertebrate viruses, bacteriophage and other dietary associated plant and insect viruses. In total, 18 new vertebrate viruses, including novel sapelovirus, astroviruses, bocaviruses, papillomaviruses and gammaherpesvirus were identified, as well as known mammalian pathogens including rabbit haemorrhagic disease virus 2 (RHDV2). Captive devils showed significantly lower levels of viral diversity than wild devils. Comparison of the two methodological approaches revealed substantial differences in the number and types of viruses detected, with meta-transcriptomics mainly identifying RNA viruses, and VLP metagenomics largely identifying DNA viruses. This study has greatly expanded our knowledge of eukaryotic viruses in the Tasmanian devil and provides important baseline information that will contribute to the conservation and captive management of this endangered species. In addition, our results showed that a combination of VLP metagenomics and meta-transcriptomics may be a more comprehensive approach to virome characterisation than either method alone.

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