The Sphagnome Project: enabling ecological and evolutionary insights through a genus-level sequencing project

David J Weston; Merritt R Turetsky; Matthew G Johnson; Gustaf Granath; Zoë Lindo; Lisa R Belyea; Steven K Rice; David T Hanson; Katharina A M Engelhardt; Jeremy Schmutz; Ellen Dorrepaal; Eugénie S Euskirchen; Hans K Stenøien; Péter Szövényi; Michelle Jackson; Bryan T Piatkowski; Wellington Muchero; Richard J Norby; Joel E Kostka; Jennifer B Glass; Håkan Rydin; Juul Limpens; Eeva-Stiina Tuittila; Kristian K Ullrich; Alyssa Carrell; Brian W Benscoter; Jin-Gui Chen; Tobi A Oke; Mats B Nilsson; Priya Ranjan; Daniel Jacobson; Erik A Lilleskov; R S Clymo; A Jonathan Shaw

doi:10.1111/nph.14860

The Sphagnome Project: enabling ecological and evolutionary insights through a genus-level sequencing project

New Phytol. 2018 Jan;217(1):16-25. doi: 10.1111/nph.14860. Epub 2017 Oct 27.

Authors

David J Weston^{1

2}, Merritt R Turetsky³, Matthew G Johnson⁴, Gustaf Granath⁵, Zoë Lindo⁶, Lisa R Belyea⁷, Steven K Rice⁸, David T Hanson⁹, Katharina A M Engelhardt¹⁰, Jeremy Schmutz^{11

12}, Ellen Dorrepaal¹³, Eugénie S Euskirchen¹⁴, Hans K Stenøien¹⁵, Péter Szövényi¹⁶, Michelle Jackson¹⁷, Bryan T Piatkowski¹⁷, Wellington Muchero¹, Richard J Norby^{2

18}, Joel E Kostka¹⁹, Jennifer B Glass¹⁹, Håkan Rydin²⁰, Juul Limpens²¹, Eeva-Stiina Tuittila²², Kristian K Ullrich²³, Alyssa Carrell¹, Brian W Benscoter²⁴, Jin-Gui Chen¹, Tobi A Oke³, Mats B Nilsson²⁵, Priya Ranjan²⁶, Daniel Jacobson¹, Erik A Lilleskov²⁷, R S Clymo²⁸, A Jonathan Shaw¹⁷

Affiliations

¹ Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA.
² Climate Change Science Institute, Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA.
³ Department of Integrative Biology, University of Guelph, Guelph, ON, N1G 2W1, Canada.
⁴ Department of Biological Sciences, Texas Tech University, Lubbock, TX, 79414, USA.
⁵ Department of Ecology, Swedish University of Agricultural Sciences, Box 7044, SE-750 07, Uppsala, Sweden.
⁶ Department of Biology, The University of Western Ontario, London, ON, N6A 5B7, Canada.
⁷ School of Geography, Queen Mary University of London, London, E1 4NS, UK.
⁸ Department of Biological Sciences, Union College, Schenectady, NY, 12308, USA.
⁹ Department of Biology, University of New Mexico, Albuquerque, NM, 87131, USA.
¹⁰ Appalachian Lab, University of Maryland Center of Environmental Science, Frostburg, MD, 21532, USA.
¹¹ HudsonAlpha Institute of Biotechnology, Huntsville, AL, 35806, USA.
¹² Department of Energy Joint Genome Institute, Walnut Creek, CA, 94598, USA.
¹³ Climate Impacts Research Center, Department of Ecology and Environmental Science, Umeå University, 98107, Abisko, Sweden.
¹⁴ Institute of Arctic Biology, University of Alaska, Fairbanks, AK, 99775, USA.
¹⁵ NTNU University Museum, Norwegian University of Science and Technology, NO-7491, Trondheim, Norway.
¹⁶ Department of Systematic and Evolutionary Botany, University of Zurich, 8008, Zurich, Switzerland.
¹⁷ Department of Biology, Duke University, Durham, NC, 27708, USA.
¹⁸ Environmental Sciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA.
¹⁹ Schools of Biology and Earth & Atmospheric Sciences, Georgia Institute of Technology, Atlanta, GA, 30332, USA.
²⁰ Department of Ecology and Genetics, Uppsala University, Norbyvägen 18D, SE-75236, Uppsala, Sweden.
²¹ Plant Ecology and Nature Conservation Group, Department of Environmental Sciences, Wageningen University, Droevendaalse steeg 3a, NL-6708 PD, Wageningen, the Netherlands.
²² Peatland and Soil Ecology Group, School of Forest Sciences, University of Eastern Finland, Joensuu, Finland.
²³ Max-Planck Institute for Evolutionary Biology, 24306, Plön, Germany.
²⁴ Department of Biological Sciences, Florida Atlantic University, Davie, FL, 33314, USA.
²⁵ Department of Forest Ecology and Management, Swedish University of Agricultural Sciences, Skogsmarksgränd, SE-901 83, Umeå, Sweden.
²⁶ Department of Plant Sciences, University of Tennessee, 2431 Joe Johnson Drive, Knoxville, TN, 37996-4561, USA.
²⁷ US Forest Service, Northern Research Station, 410 MacInnes Dr., Houghton, MI, 49931, USA.
²⁸ School of Biological & Chemical Sciences, Queen Mary University of London, London, E1 4NS, UK.

PMID: 29076547
DOI: 10.1111/nph.14860

Abstract

Considerable progress has been made in ecological and evolutionary genetics with studies demonstrating how genes underlying plant and microbial traits can influence adaptation and even 'extend' to influence community structure and ecosystem level processes. Progress in this area is limited to model systems with deep genetic and genomic resources that often have negligible ecological impact or interest. Thus, important linkages between genetic adaptations and their consequences at organismal and ecological scales are often lacking. Here we introduce the Sphagnome Project, which incorporates genomics into a long-running history of Sphagnum research that has documented unparalleled contributions to peatland ecology, carbon sequestration, biogeochemistry, microbiome research, niche construction, and ecosystem engineering. The Sphagnome Project encompasses a genus-level sequencing effort that represents a new type of model system driven not only by genetic tractability, but by ecologically relevant questions and hypotheses.

Keywords: Sphagnum; Sphagnome; ecological genomics; ecosystem engineering; evolutionary genetics; genome sequencing; niche construction; peatlands.

MeSH terms

Adaptation, Physiological
Biological Evolution
Ecology
Genome, Plant / genetics*
Genomics*
Models, Biological*
Phylogeny
Sequence Analysis, DNA
Sphagnopsida / cytology
Sphagnopsida / genetics*
Sphagnopsida / physiology