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dc.contributor.author
Blavet, Nicolas
dc.contributor.author
Blavet, Hana
dc.contributor.author
Muyle, Aline
dc.contributor.author
Käfer, Jos
dc.contributor.author
Cegan, Radim
dc.contributor.author
Deschamps, Clothilde
dc.contributor.author
Zemp, Niklaus
dc.contributor.author
Mousset, Sylvain
dc.contributor.author
Aubourg, Sebastien
dc.contributor.author
Bergero, Roberta
dc.contributor.author
Charlesworth, Deborah
dc.contributor.author
Hobza, Roman
dc.contributor.author
Widmer, Alex
dc.contributor.author
Marais, Gabriel A.B.
dc.date.accessioned
2018-10-22T11:30:49Z
dc.date.available
2017-06-11T18:46:05Z
dc.date.available
2018-10-22T11:30:49Z
dc.date.issued
2015-07-25
dc.identifier.other
10.1186/s12864-015-1698-7
en_US
dc.identifier.uri
http://hdl.handle.net/20.500.11850/103266
dc.identifier.doi
10.3929/ethz-b-000103266
dc.description.abstract
Background Silene latifolia represents one of the best-studied plant sex chromosome systems. A new approach using RNA-seq data has recently identified hundreds of new sex-linked genes in this species. However, this approach is expected to miss genes that are either not expressed or are expressed at low levels in the tissue(s) used for RNA-seq. Therefore other independent approaches are needed to discover such sex-linked genes. Results Here we used 10 well-characterized S. latifolia sex-linked genes and their homologs in Silene vulgaris, a species without sex chromosomes, to screen BAC libraries of both species. We isolated and sequenced 4 Mb of BAC clones of S. latifolia X and Y and S. vulgaris genomic regions, which yielded 59 new sex-linked genes (with S. vulgaris homologs for some of them). We assembled sequences that we believe represent the tip of the Xq arm. These sequences are clearly not pseudoautosomal, so we infer that the S. latifolia X has a single pseudoautosomal region (PAR) on the Xp arm. The estimated mean gene density in X BACs is 2.2 times lower than that in S. vulgaris BACs, agreeing with the genome size difference between these species. Gene density was estimated to be extremely low in the Y BAC clones. We compared our BAC-located genes with the sex-linked genes identified in previous RNA-seq studies, and found that about half of them (those with low expression in flower buds) were not identified as sex-linked in previous RNA-seq studies. We compiled a set of ~70 validated X/Y genes and X-hemizygous genes (without Y copies) from the literature, and used these genes to show that X-hemizygous genes have a higher probability of being undetected by the RNA-seq approach, compared with X/Y genes; we used this to estimate that about 30 % of our BAC-located genes must be X-hemizygous. The estimate is similar when we use BAC-located genes that have S. vulgaris homologs, which excludes genes that were gained by the X chromosome. Conclusions Our BAC sequencing identified 59 new sex-linked genes, and our analysis of these BAC-located genes, in combination with RNA-seq data suggests that gene losses from the S. latifolia Y chromosome could be as high as 30 %, higher than previous estimates of 10-20 %.
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
Sex chromosomes
en_US
dc.subject
Sex-linked genes
en_US
dc.subject
Plant
en_US
dc.subject
BAC
en_US
dc.subject
RNA-seq
en_US
dc.subject
Gene loss
en_US
dc.subject
Y degeneration
en_US
dc.subject
Silene latifolia
en_US
dc.subject
Silene vulgaris
en_US
dc.title
Identifying new sex-linked genes through BAC sequencing in the dioecious plant Silene latifolia
en_US
dc.type
Journal Article
dc.rights.license
Creative Commons Attribution 4.0 International
ethz.journal.title
BMC Genomics
ethz.journal.volume
16
en_US
ethz.pages.start
546
en_US
ethz.size
8 p.
en_US
ethz.version.deposit
publishedVersion
en_US
ethz.identifier.wos
ethz.identifier.nebis
004256340
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::02350 - Dep. Umweltsystemwissenschaften / Dep. of Environmental Systems Science::02720 - Institut für Integrative Biologie / Institute of Integrative Biology::03706 - Widmer, Alexander / Widmer, Alexander
en_US
ethz.leitzahl.certified
ETH Zürich::00002 - ETH Zürich::00012 - Lehre und Forschung::00007 - Departemente::02350 - Dep. Umweltsystemwissenschaften / Dep. of Environmental Systems Science::02720 - Institut für Integrative Biologie / Institute of Integrative Biology::03706 - Widmer, Alexander / Widmer, Alexander
ethz.date.deposited
2017-06-11T18:46:08Z
ethz.source
ECIT
ethz.identifier.importid
imp59365363b1f9975218
ethz.ecitpid
pub:161477
ethz.eth
yes
en_US
ethz.availability
Open access
en_US
ethz.rosetta.installDate
2017-07-19T10:41:15Z
ethz.rosetta.lastUpdated
2018-12-03T01:30:21Z
ethz.rosetta.exportRequired
true
ethz.rosetta.versionExported
true
ethz.COinS
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