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A transcriptome for the early-branching fern Botrychium lunaria enables fine-grained resolution of population structure

Vinciane Mossion, Benjamin Dauphin, Jason Grant, Niklaus Zemp, View ORCID ProfileDaniel Croll
doi: https://doi.org/10.1101/2020.02.17.952283
Vinciane Mossion
1Laboratory of Evolutionary Genetics, University of Neuchâtel, Neuchâtel, Switzerland
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Benjamin Dauphin
1Laboratory of Evolutionary Genetics, University of Neuchâtel, Neuchâtel, Switzerland
2Swiss Federal Research Institute WSL, Birmensdorf, Switzerland
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Jason Grant
1Laboratory of Evolutionary Genetics, University of Neuchâtel, Neuchâtel, Switzerland
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Niklaus Zemp
3Genetic Diversity Centre (GDC), ETH Zurich, Zurich, Switzerland
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Daniel Croll
1Laboratory of Evolutionary Genetics, University of Neuchâtel, Neuchâtel, Switzerland
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  • ORCID record for Daniel Croll
  • For correspondence: daniel.croll@unine.ch
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Abstract

Ferns are the second most dominant group of land plants after angiosperms. Extant species occupy an extensive range of habitats and contribute significantly to ecosystem functioning. Despite the importance of ferns, most taxa are poorly covered by genomic resources. The genus Botrychium belongs to the family Ophioglossaceae, one of the earliest divergent lineages of vascular plants, and has a cosmopolitan distribution with 35 species, half of which are polyploids. Here, we establish a transcriptome for Botrychium lunaria, a diploid species with an extremely large genome with a 1C value of 12.10 pg. We assembled 25,701 high-quality transcripts with an average length of 1,332 bp based on deep RNA-sequencing of a single individual. We sequenced an additional 11 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 374,510 single nucleotide polymorphisms (SNPs) segregating among individuals for an average density of 14 SNPs per kb. 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 90 taxa representing all fern orders to ascertain the placement of the genus Botrychium. The high-quality transcriptomic resources enable powerful population and phylogenomic studies in an important group of ferns.

Significance statement Ferns pose substantial puzzles in terms of lifestyles, genome organization and population structure. Progress has been significantly hampered by the lack of genomic resources. Here, we present a transcriptome for Botrychium lunaria, a phylogenetically early-branching fern with an extremely large genome. We show that the new transcriptome improves phylogenetic resolution among early-branching ferns. Based on an additional 11 transcriptomes of the same species, we identify unexpected variation in population-level heterozygosity.

Competing Interest Statement

The authors have declared no competing interest.

Footnotes

  • Updated phylogenomics analyses, intra-individual polymorphism analyses, text revisions.

Copyright 
The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY-NC-ND 4.0 International license.
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Posted July 25, 2020.
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A transcriptome for the early-branching fern Botrychium lunaria enables fine-grained resolution of population structure
Vinciane Mossion, Benjamin Dauphin, Jason Grant, Niklaus Zemp, Daniel Croll
bioRxiv 2020.02.17.952283; doi: https://doi.org/10.1101/2020.02.17.952283
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A transcriptome for the early-branching fern Botrychium lunaria enables fine-grained resolution of population structure
Vinciane Mossion, Benjamin Dauphin, Jason Grant, Niklaus Zemp, Daniel Croll
bioRxiv 2020.02.17.952283; doi: https://doi.org/10.1101/2020.02.17.952283

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