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dc.contributor.author
Milosavljevic, Stefan
dc.contributor.author
Kuo, Tony
dc.contributor.author
Decarli, Samuele
dc.contributor.author
Mohn, Lucas
dc.contributor.author
Sese, Jun
dc.contributor.author
Shimizu, Kentaro K.
dc.contributor.author
Shimizu-Inatsugi, Rie
dc.contributor.author
Robinson, Mark D.
dc.date.accessioned
2021-09-02T11:27:04Z
dc.date.available
2021-07-29T03:31:46Z
dc.date.available
2021-09-02T11:27:04Z
dc.date.issued
2021-12
dc.identifier.issn
1471-2164
dc.identifier.other
10.1186/s12864-021-07845-2
en_US
dc.identifier.uri
http://hdl.handle.net/20.500.11850/498291
dc.identifier.doi
10.3929/ethz-b-000498291
dc.description.abstract
Background: Whole genome duplication (WGD) events are common in the evolutionary history of many living organisms. For decades, researchers have been trying to understand the genetic and epigenetic impact of WGD and its underlying molecular mechanisms. Particular attention was given to allopolyploid study systems, species resulting from an hybridization event accompanied by WGD. Investigating the mechanisms behind the survival of a newly formed allopolyploid highlighted the key role of DNA methylation. With the improvement of high-throughput methods, such as whole genome bisulfite sequencing (WGBS), an opportunity opened to further understand the role of DNA methylation at a larger scale and higher resolution. However, only a few studies have applied WGBS to allopolyploids, which might be due to lack of genomic resources combined with a burdensome data analysis process. To overcome these problems, we developed the Automated Reproducible Polyploid EpiGenetic GuIdance workflOw (ARPEGGIO): the first workflow for the analysis of epigenetic data in polyploids. This workflow analyzes WGBS data from allopolyploid species via the genome assemblies of the allopolyploid’s parent species. ARPEGGIO utilizes an updated read classification algorithm (EAGLE-RC), to tackle the challenge of sequence similarity amongst parental genomes. ARPEGGIO offers automation, but more importantly, a complete set of analyses including spot checks starting from raw WGBS data: quality checks, trimming, alignment, methylation extraction, statistical analyses and downstream analyses. A full run of ARPEGGIO outputs a list of genes showing differential methylation. ARPEGGIO was made simple to set up, run and interpret, and its implementation ensures reproducibility by including both package management and containerization. Results: We evaluated ARPEGGIO in two ways. First, we tested EAGLE-RC’s performance with publicly available datasets given a ground truth, and we show that EAGLE-RC decreases the error rate by 3 to 4 times compared to standard approaches. Second, using the same initial dataset, we show agreement between ARPEGGIO’s output and published results. Compared to other similar workflows, ARPEGGIO is the only one supporting polyploid data. Conclusions: The goal of ARPEGGIO is to promote, support and improve polyploid research with a reproducible and automated set of analyses in a convenient implementation. ARPEGGIO is available at https://github.com/supermaxiste/ARPEGGIO.
en_US
dc.format
application/pdf
en_US
dc.language.iso
en
en_US
dc.publisher
BioMed Central
en_US
dc.rights.uri
http://creativecommons.org/licenses/by/4.0/
dc.subject
Snakemake
en_US
dc.subject
Epigenetics
en_US
dc.subject
Bisulfite-sequencing
en_US
dc.subject
Polyploidy
en_US
dc.subject
Allopolyploids
en_US
dc.subject
Reproducibility
en_US
dc.subject
Reproducibility
en_US
dc.subject
Workflow
en_US
dc.subject
Dna-methylation
en_US
dc.subject
Whole-genome-bisulfite-sequencing
en_US
dc.title
ARPEGGIO: Automated Reproducible Polyploid EpiGenetic GuIdance workflOw
en_US
dc.type
Journal Article
dc.rights.license
Creative Commons Attribution 4.0 International
dc.date.published
2021-07-17
ethz.journal.title
MC genomics
ethz.journal.volume
22
en_US
ethz.journal.issue
1
en_US
ethz.pages.start
547
en_US
ethz.size
12 p.
en_US
ethz.version.deposit
publishedVersion
en_US
ethz.identifier.wos
ethz.identifier.scopus
ethz.publication.place
London
en_US
ethz.publication.status
published
en_US
ethz.leitzahl
ETH Zürich::00002 - ETH Zürich::00012 - Lehre und Forschung::00007 - Departemente::02150 - Dep. Informatik / Dep. of Computer Science
en_US
ethz.date.deposited
2021-07-29T03:31:53Z
ethz.source
SCOPUS
ethz.eth
yes
en_US
ethz.availability
Open access
en_US
ethz.rosetta.installDate
2021-09-02T11:27:11Z
ethz.rosetta.lastUpdated
2022-03-29T11:27:19Z
ethz.rosetta.versionExported
true
ethz.COinS
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