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dc.contributor.author
Mossion, Vinciane
dc.contributor.author
Dauphin, Benjamin
dc.contributor.author
Grant, Jason
dc.contributor.author
Kessler, Michael
dc.contributor.author
Zemp, Niklaus
dc.contributor.author
Croll, Daniel
dc.date.accessioned
2022-01-14T10:48:29Z
dc.date.available
2021-08-18T02:37:01Z
dc.date.available
2021-09-23T08:23:29Z
dc.date.available
2022-01-14T10:48:29Z
dc.date.issued
2022-01
dc.identifier.issn
1755-098X
dc.identifier.issn
1755-0998
dc.identifier.other
10.1111/1755-0998.13478
en_US
dc.identifier.uri
http://hdl.handle.net/20.500.11850/501213
dc.identifier.doi
10.3929/ethz-b-000501213
dc.description.abstract
Ferns are the second most diverse group of land plants after angiosperms. Extant species occupy a wide range of habitats and contribute significantly to ecosystem functioning. Despite the importance of ferns, most taxa are poorly covered by genomic resources and within-species studies based on high-resolution markers are entirely lacking. The genus Botrychium belongs to the family Ophioglossaceae, which includes species with very large genomes and chromosome numbers (e.g., Ophioglossum reticulatum 2n = 1520). The genus has a cosmopolitan distribution with 35 species, half of which are polyploids. Here, we establish a transcriptome for Botrychium lunaria (L.) Sw., a diploid species with an extremely large genome of about similar to 19.0-23.7 Gb. We assembled 25,677 high-quality transcripts with an average length of 1,333 bp based on deep RNA-sequencing of a single individual. We sequenced 11 additional transcriptomes of individuals from two populations in Switzerland, including the population of the reference individual. Based on read mapping to reference transcript sequences, we identified 374,463 single nucleotide polymorphisms (SNPs) segregating among individuals for an average density of 14 SNPs per kilobase. We found that all 12 transcriptomes were most likely from diploid individuals. The transcriptome-wide markers provided unprecedented resolution of the population genetic structure, revealing substantial variation in heterozygosity among individuals. We also constructed a phylogenomic tree of 92 taxa representing all fern orders to ascertain the placement of the genus Botrychium. High-quality transcriptomic resources and SNP sets constitute powerful population genomic resources to investigate the ecology, and evolution of fern populations.
en_US
dc.format
application/pdf
en_US
dc.language.iso
en
en_US
dc.publisher
Wiley
en_US
dc.rights.uri
http://creativecommons.org/licenses/by-nc/4.0/
dc.subject
ferns
en_US
dc.subject
Ophioglossaceae
en_US
dc.subject
population genomics
en_US
dc.subject
SNP development
en_US
dc.subject
transcriptome assembly
en_US
dc.title
Transcriptome-wide SNPs for Botrychium lunaria ferns enable fine-grained analysis of ploidy and population structure
en_US
dc.type
Journal Article
dc.rights.license
Creative Commons Attribution-NonCommercial 4.0 International
dc.date.published
2021-07-26
ethz.journal.title
Molecular Ecology Resources
ethz.journal.volume
22
en_US
ethz.journal.issue
1
en_US
ethz.journal.abbreviated
Mol. Ecol. Resour.
ethz.pages.start
254
en_US
ethz.pages.end
271
en_US
ethz.version.deposit
publishedVersion
en_US
ethz.identifier.wos
ethz.identifier.scopus
ethz.publication.place
Oxford
en_US
ethz.publication.status
published
en_US
ethz.date.deposited
2021-08-18T02:37:29Z
ethz.source
WOS
ethz.eth
yes
en_US
ethz.availability
Open access
en_US
ethz.rosetta.installDate
2022-01-14T10:48:36Z
ethz.rosetta.lastUpdated
2023-02-06T23:49:46Z
ethz.rosetta.exportRequired
true
ethz.rosetta.versionExported
true
ethz.COinS
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