Transcriptome‐wide SNPs for Botrychium lunaria ferns enable fine‐grained analysis of ploidy and population structure
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-...
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ftunivzuerich:oai:www.zora.uzh.ch:205610 2024-10-13T14:06:26+00:00 Transcriptome‐wide SNPs for Botrychium lunaria ferns enable fine‐grained analysis of ploidy and population structure Mossion, Vinciane Dauphin, Benjamin Grant, Jason Kessler, Michael Zemp, Niklaus Croll, Daniel 2022-01-01 application/pdf https://www.zora.uzh.ch/id/eprint/205610/ eng eng Wiley-Blackwell Publishing, Inc. https://www.zora.uzh.ch/id/eprint/205610/1/1755-0998.13478.pdf doi:10.5167/uzh-205610 doi:10.1111/1755-0998.13478 info:pmid/34310066 urn:issn:1755-0998 info:eu-repo/semantics/openAccess Creative Commons: Attribution-NonCommercial 4.0 International (CC BY-NC 4.0) http://creativecommons.org/licenses/by-nc/4.0/ Mossion, Vinciane; Dauphin, Benjamin; Grant, Jason; Kessler, Michael; Zemp, Niklaus; Croll, Daniel (2022). Transcriptome‐wide SNPs for Botrychium lunaria ferns enable fine‐grained analysis of ploidy and population structure. Molecular Ecology Resources, 22(1):254-271. Department of Systematic and Evolutionary Botany Zurich-Basel Plant Science Center 580 Plants (Botany) Biotechnology Genetics Ecology Evolution Behavior and Systematics Journal Article PeerReviewed info:eu-repo/semantics/article info:eu-repo/semantics/publishedVersion 2022 ftunivzuerich https://doi.org/10.5167/uzh-20561010.1111/1755-0998.13478 2024-10-02T15:06:30Z 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 ~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. Article in Journal/Newspaper Botrychium lunaria University of Zurich (UZH): ZORA (Zurich Open Repository and Archive |
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Open Polar |
collection |
University of Zurich (UZH): ZORA (Zurich Open Repository and Archive |
op_collection_id |
ftunivzuerich |
language |
English |
topic |
Department of Systematic and Evolutionary Botany Zurich-Basel Plant Science Center 580 Plants (Botany) Biotechnology Genetics Ecology Evolution Behavior and Systematics |
spellingShingle |
Department of Systematic and Evolutionary Botany Zurich-Basel Plant Science Center 580 Plants (Botany) Biotechnology Genetics Ecology Evolution Behavior and Systematics Mossion, Vinciane Dauphin, Benjamin Grant, Jason Kessler, Michael Zemp, Niklaus Croll, Daniel Transcriptome‐wide SNPs for Botrychium lunaria ferns enable fine‐grained analysis of ploidy and population structure |
topic_facet |
Department of Systematic and Evolutionary Botany Zurich-Basel Plant Science Center 580 Plants (Botany) Biotechnology Genetics Ecology Evolution Behavior and Systematics |
description |
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 ~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. |
format |
Article in Journal/Newspaper |
author |
Mossion, Vinciane Dauphin, Benjamin Grant, Jason Kessler, Michael Zemp, Niklaus Croll, Daniel |
author_facet |
Mossion, Vinciane Dauphin, Benjamin Grant, Jason Kessler, Michael Zemp, Niklaus Croll, Daniel |
author_sort |
Mossion, Vinciane |
title |
Transcriptome‐wide SNPs for Botrychium lunaria ferns enable fine‐grained analysis of ploidy and population structure |
title_short |
Transcriptome‐wide SNPs for Botrychium lunaria ferns enable fine‐grained analysis of ploidy and population structure |
title_full |
Transcriptome‐wide SNPs for Botrychium lunaria ferns enable fine‐grained analysis of ploidy and population structure |
title_fullStr |
Transcriptome‐wide SNPs for Botrychium lunaria ferns enable fine‐grained analysis of ploidy and population structure |
title_full_unstemmed |
Transcriptome‐wide SNPs for Botrychium lunaria ferns enable fine‐grained analysis of ploidy and population structure |
title_sort |
transcriptome‐wide snps for botrychium lunaria ferns enable fine‐grained analysis of ploidy and population structure |
publisher |
Wiley-Blackwell Publishing, Inc. |
publishDate |
2022 |
url |
https://www.zora.uzh.ch/id/eprint/205610/ |
genre |
Botrychium lunaria |
genre_facet |
Botrychium lunaria |
op_source |
Mossion, Vinciane; Dauphin, Benjamin; Grant, Jason; Kessler, Michael; Zemp, Niklaus; Croll, Daniel (2022). Transcriptome‐wide SNPs for Botrychium lunaria ferns enable fine‐grained analysis of ploidy and population structure. Molecular Ecology Resources, 22(1):254-271. |
op_relation |
https://www.zora.uzh.ch/id/eprint/205610/1/1755-0998.13478.pdf doi:10.5167/uzh-205610 doi:10.1111/1755-0998.13478 info:pmid/34310066 urn:issn:1755-0998 |
op_rights |
info:eu-repo/semantics/openAccess Creative Commons: Attribution-NonCommercial 4.0 International (CC BY-NC 4.0) http://creativecommons.org/licenses/by-nc/4.0/ |
op_doi |
https://doi.org/10.5167/uzh-20561010.1111/1755-0998.13478 |
_version_ |
1812812587388108800 |