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dc.contributor.author
Arbore, Roberto
dc.contributor.author
Sekii, Kiyono
dc.contributor.author
Beisel, Christian
dc.date.accessioned
2019-06-07T10:40:21Z
dc.date.available
2017-06-11T18:23:26Z
dc.date.available
2019-06-07T10:40:21Z
dc.date.issued
2015-07-03
dc.identifier.issn
1742-9994
dc.identifier.other
10.1186/s12983-015-0106-0
en_US
dc.identifier.uri
http://hdl.handle.net/20.500.11850/102522
dc.identifier.doi
10.3929/ethz-b-000102522
dc.description.abstract
Introduction RNA interference (RNAi) of trait-specific genes permits the manipulation of specific phenotypic traits (“phenotypic engineering”) and thus represents a powerful tool to test trait function in evolutionary studies. The identification of suitable candidate genes, however, often relies on existing functional gene annotation, which is usually limited in emerging model organisms, especially when they are only distantly related to traditional genetic model organisms. A case in point is the free-living flatworm Macrostomum lignano (Lophotrochozoa: Platyhelminthes: Rhabditophora), an increasingly powerful model organism for evolutionary studies of sex in simultaneous hermaphrodites. To overcome the limitation of sparse functional annotation, we have performed a positional RNA-Seq analysis on different body fragments in order to identify organ-specific candidate transcripts. We then performed gene expression (in situ hybridization) and gene function (RNAi) analyses on 23 candidate transcripts, both to evaluate the predictive potential of this approach and to obtain preliminary functional characterizations of these candidate genes. Results We identified over 4000 transcripts that could be expected to show specific expression in different reproductive organs (including testis, ovary and the male and female genital systems). The predictive potential of the method could then be verified by confirming organ-specific expression for several candidate transcripts, some of which yielded interesting trait-specific knock-down phenotypes that can now be followed up in future phenotypic engineering studies. Conclusions Our positional RNA-Seq analysis represents a highly useful resource for the identification of candidate transcripts for functional and phenotypic engineering studies in M. lignano, and it has already been used successfully in several studies. Moreover, this approach can overcome some inherent limitations of homology-based candidate selection and thus should be applicable to a broad range of emerging model organisms.
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
Phenotypic engineering
en_US
dc.subject
RNA-Seq
en_US
dc.subject
RNA interference
en_US
dc.subject
Simultaneous hermaphrodite
en_US
dc.subject
Macrostomum lignano
en_US
dc.title
Positional RNA-Seq identifies candidate genes for phenotypic engineering of sexual traits
en_US
dc.type
Journal Article
dc.rights.license
Creative Commons Attribution 4.0 International
ethz.journal.title
Frontiers in Zoology
ethz.journal.volume
12
en_US
ethz.journal.abbreviated
Front. zool.
ethz.pages.start
14
en_US
ethz.pages.end
1
en_US
ethz.size
16 p.
en_US
ethz.version.deposit
publishedVersion
en_US
ethz.identifier.wos
ethz.identifier.nebis
010180756
ethz.publication.place
London
en_US
ethz.publication.status
published
en_US
ethz.date.deposited
2017-06-11T18:24:04Z
ethz.source
ECIT
ethz.identifier.importid
imp593653526f33015098
ethz.ecitpid
pub:160662
ethz.eth
yes
en_US
ethz.availability
Open access
en_US
ethz.rosetta.installDate
2017-07-12T17:26:40Z
ethz.rosetta.lastUpdated
2019-06-07T10:40:33Z
ethz.rosetta.versionExported
true
ethz.COinS
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