About: Sequencing the Genome of Indian Flying Fox, Natural Reservoir of Nipah Virus, Using Hybrid Assembly and Conservative Secondary Scaffolding

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About: Sequencing the Genome of Indian Flying Fox, Natural Reservoir of Nipah Virus, Using Hybrid Assembly and Conservative Secondary Scaffolding Goto Sponge NotDistinct Permalink

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

Attributes	Values
type	Academic Article research paper schema:ScholarlyArticle
isDefinedBy	Covid-on-the-Web dataset
title	Sequencing the Genome of Indian Flying Fox, Natural Reservoir of Nipah Virus, Using Hybrid Assembly and Conservative Secondary Scaffolding
Creator	Horvat, Branka Legras-Lachuer, Catherine Bailly-Bechet, Marc Irving, Aaron Aurine, Noémie Fouret, Julien Bailly-Bechet, J-N Binet, Martin Brunet, Frédéric Croze, Séverine Enchéry, Francois Fg, Brunet Fouret, J Goumaidi, Abdelghafar Guinier, Marie Lachuer, Joël Me, Julien@fouret Preininger, Doris Volff, Jean-Nicolas
source	Medline; PMC
abstract	Indian fruit bats, flying fox Pteropus medius was identified as an asymptomatic natural host of recently emerged Nipah virus, which is known to induce a severe infectious disease in humans. The absence of P. medius genome sequence presents an important obstacle for further studies of virus–host interactions and better understanding of mechanisms of zoonotic viral emergence. Generation of the high-quality genome sequence is often linked to a considerable effort associated to elevated costs. Although secondary scaffolding methods have reduced sequencing expenses, they imply the development of new tools for the integration of different data sources to achieve more reliable sequencing results. We initially sequenced the P. medius genome using the combination of Illumina paired-end and Nanopore sequencing, with a depth of 57.4x and 6.1x, respectively. Then, we introduced the novel scaff2link software to integrate multiple sources of information for secondary scaffolding, allowing to remove the association with discordant information among two sources. Different quality metrics were next produced to validate the benefits from secondary scaffolding. The P. medius genome, assembled by this method, has a length of 1,985 Mb and consists of 33,613 contigs and 16,113 scaffolds with an NG50 of 19 Mb. At least 22.5% of the assembled sequences is covered by interspersed repeats already described in other species and 19,823 coding genes are annotated. Phylogenetic analysis demonstrated the clustering of P. medius genome with two other Pteropus bat species, P. alecto and P. vampyrus, for which genome sequences are currently available. SARS-CoV entry receptor ACE2 sequence of P. medius was 82.7% identical with ACE2 of Rhinolophus sinicus bats, thought to be the natural host of SARS-CoV. Altogether, our results confirm that a lower depth of sequencing is enough to obtain a valuable genome sequence, using secondary scaffolding approaches and demonstrate the benefits of the scaff2link application. The genome sequence is now available to the scientific community to (i) proceed with further genomic analysis of P. medius, (ii) to characterize the underlying mechanism allowing Nipah virus maintenance and perpetuation in its bat host, and (iii) to monitor their evolutionary pathways toward a better understanding of bats’ ability to control viral infections.
has issue date	2020-07-29(xsd:dateTime)
bibo:doi	10.3389/fmicb.2020.01807
bibo:pmid	32849415
has license	cc-by
sha1sum (hex)	fb51414289fa361cd27d00a7d821c61d418dac4b
schema:url	https://doi.org/10.3389/fmicb.2020.01807
resource representing a document's title	Sequencing the Genome of Indian Flying Fox, Natural Reservoir of Nipah Virus, Using Hybrid Assembly and Conservative Secondary Scaffolding
has PubMed Central identifier	PMC7403528
has PubMed identifier	32849415
schema:publication	Front Microbiol
resource representing a document's body	covid:fb51414289fa361cd27d00a7d821c61d418dac4b#body_text
is schema:about of	named entity 'demonstrated' named entity 'Pteropus' named entity 'interactions' named entity 'sequences' named entity 'covered' named entity 'viral' named entity 'Sequencing' named entity 'Genome' named entity 'BAT' named entity 'ORG' named entity 'VIRAL' named entity 'ASSOCIATED' named entity 'SCAFFOLDING' named entity 'LENGTH' named entity 'OUR' named entity 'RECENTLY' named entity 'PHYLOGENETIC ANALYSIS' named entity 'IDENTICAL' named entity 'REDUCED' named entity 'INITIALLY' named entity 'CONFIRM' named entity 'NOVEL' named entity 'COVERED BY' named entity 'QUALITY METRICS' named entity 'KNOWN' named entity 'asymptomatic' named entity 'secondary' named entity 'costs' named entity 'severe' named entity 'genes' named entity 'emerged' named entity 'tools' named entity 'Nanopore sequencing' named entity 'genome' named entity 'P. alecto' named entity 'validate' named entity 'contigs' named entity 'genome' named entity 'Fox' named entity 'SARS-CoV' named entity 'Pteropus' named entity 'asymptomatic' named entity 'genome sequence' named entity 'infectious disease' named entity 'virus' named entity 'P. alecto' named entity 'ACE2' named entity 'Rhinolophus sinicus' named entity 'natural host' named entity 'Hybrid Assembly' named entity 'isoform' named entity 'Rhinolophus sinicus' named entity 'genome annotation' named entity 'bat' named entity 'ENA' named entity 'P. alecto' named entity '+358' named entity 'NGS' named entity 'RefSeq' named entity 'SAMtools' named entity 'homology' named entity 'Promega' named entity 'gene'

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