Show simple item record

dc.contributor.author
Chenuil, Anne
dc.contributor.author
Hoareau, Thierry B.
dc.contributor.author
Egea, Emilie
dc.contributor.author
Penant, Gwilherm
dc.contributor.author
Rocher, Caroline
dc.contributor.author
Aurelle, Didier
dc.contributor.author
Mokhtar-Jamai, Kenza
dc.contributor.author
Bishop, John D. D.
dc.contributor.author
Boissin, Emilie
dc.contributor.author
Diaz, Angie
dc.contributor.author
Krakau, Manuela
dc.contributor.author
Luttikhuizen, Pieternella C.
dc.contributor.author
Patti, Francesco P.
dc.contributor.author
Blavet, Nicolas
dc.contributor.author
Mousset, Sylvain
dc.date.accessioned
2018-05-23T10:43:30Z
dc.date.available
2017-06-09T06:02:20Z
dc.date.available
2018-05-23T10:43:30Z
dc.date.issued
2010-09-13
dc.identifier.issn
1471-2148
dc.identifier.other
10.1186/1471-2148-10-276
en_US
dc.identifier.uri
http://hdl.handle.net/20.500.11850/23708
dc.identifier.doi
10.3929/ethz-b-000023708
dc.description.abstract
Background Despite the impressive growth of sequence databases, the limited availability of nuclear markers that are sufficiently polymorphic for population genetics and phylogeography and applicable across various phyla restricts many potential studies, particularly in non-model organisms. Numerous introns have invariant positions among kingdoms, providing a potential source for such markers. Unfortunately, most of the few known EPIC (Exon Primed Intron Crossing) loci are restricted to vertebrates or belong to multigenic families. Results In order to develop markers with broad applicability, we designed a bioinformatic approach aimed at avoiding multigenic families while identifying intron positions conserved across metazoan phyla. We developed a program facilitating the identification of EPIC loci which allowed slight variation in intron position. From the Homolens databases we selected 29 gene families which contained 52 promising introns for which we designed 93 primer pairs. PCR tests were performed on several ascidians, echinoderms, bivalves and cnidarians. On average, 24 different introns per genus were amplified in bilaterians. Remarkably, five of the introns successfully amplified in all of the metazoan genera tested (a dozen genera, including cnidarians). The influence of several factors on amplification success was investigated. Success rate was not related to the phylogenetic relatedness of a taxon to the groups that most influenced primer design, showing that these EPIC markers are extremely conserved in animals. Conclusions Our new method now makes it possible to (i) rapidly isolate a set of EPIC markers for any phylum, even outside the animal kingdom, and thus, (ii) compare genetic diversity at potentially homologous polymorphic loci between divergent taxa.
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/2.0/
dc.subject
Intron Position
en_US
dc.subject
Protein Alignment
en_US
dc.subject
Epic Locus
en_US
dc.subject
Nucleotide Alignment
en_US
dc.subject
Intron Locus
en_US
dc.title
An efficient method to find potentially universal population genetic markers, applied to metazoans
en_US
dc.type
Journal Article
dc.rights.license
Creative Commons Attribution 2.0 Generic
ethz.journal.title
BMC Evolutionary Biology
ethz.journal.volume
10
en_US
ethz.journal.abbreviated
BMC evol. biol.
ethz.pages.start
276
en_US
ethz.size
17 p.
en_US
ethz.version.deposit
publishedVersion
en_US
ethz.identifier.wos
ethz.identifier.nebis
004100194
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
2017-06-09T06:02:27Z
ethz.source
ECIT
ethz.identifier.importid
imp59364d193dee269812
ethz.ecitpid
pub:38777
ethz.eth
yes
en_US
ethz.availability
Open access
en_US
ethz.rosetta.installDate
2017-07-18T13:55:57Z
ethz.rosetta.lastUpdated
2018-11-07T09:29:40Z
ethz.rosetta.exportRequired
true
ethz.rosetta.versionExported
true
ethz.COinS
ctx_ver=Z39.88-2004&rft_val_fmt=info:ofi/fmt:kev:mtx:journal&rft.atitle=An%20efficient%20method%20to%20find%20potentially%20universal%20population%20genetic%20markers,%20applied%20to%20metazoans&rft.jtitle=BMC%20Evolutionary%20Biology&rft.date=2010-09-13&rft.volume=10&rft.spage=276&rft.issn=1471-2148&rft.au=Chenuil,%20Anne&Hoareau,%20Thierry%20B.&Egea,%20Emilie&Penant,%20Gwilherm&Rocher,%20Caroline&rft.genre=article&
 Search via SFX

Files in this item

Thumbnail

Publication type

Show simple item record