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Combining epiGBS markers with long read transcriptome sequencing to assess differentiation associated with habitat in Reynoutria (aka Fallopia)

View ORCID ProfileMarta Robertson, Mariano Alvarez, Thomas van Gurp, View ORCID ProfileCornelis A. M. Wagemaker, Fahong Yu, David Moraga Amador, View ORCID ProfileWilliam G. Farmerie, View ORCID ProfileKoen J. F. Verhoeven, View ORCID ProfileChristina L. Richards
doi: https://doi.org/10.1101/2020.09.30.317966
Marta Robertson
1Agroscope, Nyon, Switzerland
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Mariano Alvarez
2Department of Biology, Duke University, Durham, NC, 27708 USA
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Thomas van Gurp
3Department of Terrestrial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), Wageningen, The Netherlands
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Cornelis A. M. Wagemaker
4Department of Experimental Plant Ecology, Radboud University, Nijmegen, The Netherlands
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Fahong Yu
5Nextgen DNA sequencing laboratory, University of Florida, Gainesville, FL 32610 USA
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David Moraga Amador
5Nextgen DNA sequencing laboratory, University of Florida, Gainesville, FL 32610 USA
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William G. Farmerie
5Nextgen DNA sequencing laboratory, University of Florida, Gainesville, FL 32610 USA
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Koen J. F. Verhoeven
6Department of Terrestrial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), Wageningen, the Netherlands
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Christina L. Richards
7Department of Integrative Biology, University of South Florida, Tampa, FL 33620 USA; Plant Evolutionary Ecology group, University of Tübingen, D-72076 Tübingen, Germany
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  • For correspondence: clr@usf.edu
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Summary

Despite the limitations of genetic bottlenecks, several invasive species appear to thrive in non-native ranges with extremely low levels of sequence-based genetic variation. We previously demonstrated differentiation of DNA methylation to habitat types of the highly clonal, genetically depauperate Japanese knotweeds using anonymous markers, but the functional relevance of this DNA methylation variation is unknown. Here, we sequenced the full transcriptome combined with a reduced representation bisulfite sequencing approach, epigenotyping by sequencing (epiGBS), to characterize the association among DNA methylation, functional transcripts and the diverse habitat types occupied by the invasive Reynoutria species. We identified 50,435 putative transcripts overall, of which 48,866 were annotated with the NCBI NR database. Of these 17,872 (35%) and 16,122 (32%) transcripts shared sequence identity with Arabidopsis thaliana and Beta vulgaris, respectively. We found genetic differentiation by habitat type suggesting the action of selection and a marginal pattern of differentiation of DNA methylation among habitats, which appears to be associated with sequence differences. However, we found no individual methylation loci associated with habitat, limiting our ability to make functional interpretations. Regardless of the source of variation in DNA methylation, these changes may represent an important component of the response to environmental conditions, particularly in highly clonal plants, but more fine scale genomics analysis is required to test if DNA methylation variation in this system is responsible for functional divergence.

Competing Interest Statement

The authors have declared no competing interest.

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-ND 4.0 International license.
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Posted October 01, 2020.
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Combining epiGBS markers with long read transcriptome sequencing to assess differentiation associated with habitat in Reynoutria (aka Fallopia)
Marta Robertson, Mariano Alvarez, Thomas van Gurp, Cornelis A. M. Wagemaker, Fahong Yu, David Moraga Amador, William G. Farmerie, Koen J. F. Verhoeven, Christina L. Richards
bioRxiv 2020.09.30.317966; doi: https://doi.org/10.1101/2020.09.30.317966
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Combining epiGBS markers with long read transcriptome sequencing to assess differentiation associated with habitat in Reynoutria (aka Fallopia)
Marta Robertson, Mariano Alvarez, Thomas van Gurp, Cornelis A. M. Wagemaker, Fahong Yu, David Moraga Amador, William G. Farmerie, Koen J. F. Verhoeven, Christina L. Richards
bioRxiv 2020.09.30.317966; doi: https://doi.org/10.1101/2020.09.30.317966

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