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Guzman-Torres CR, Trybulec E, LeVasseur H, Akella H, Amee M, Strickland E, Pauloski N, Williams M, Romero-Severson J, Hoban S, Woeste K, Pike CC, Fetter KC, Webster CN, Neitzey ML, O’Neill RJ, Wegrzyn JL. Conserving a threatened North American walnut: a chromosome-scale reference genome for butternut (Juglans cinerea). G3 (Bethesda) 2024; 14:jkad189. [PMID: 37703053 PMCID: PMC10849370 DOI: 10.1093/g3journal/jkad189] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/23/2023] [Revised: 05/23/2023] [Accepted: 07/28/2023] [Indexed: 09/14/2023]
Abstract
With the advent of affordable and more accurate third-generation sequencing technologies, and the associated bioinformatic tools, it is now possible to sequence, assemble, and annotate more species of conservation concern than ever before. Juglans cinerea, commonly known as butternut or white walnut, is a member of the walnut family, native to the Eastern United States and Southeastern Canada. The species is currently listed as Endangered on the IUCN Red List due to decline from an invasive fungus known as Ophiognomonia clavigignenti-juglandacearum (Oc-j) that causes butternut canker. Oc-j creates visible sores on the trunks of the tree which essentially starves and slowly kills the tree. Natural resistance to this pathogen is rare. Conserving butternut is of utmost priority due to its critical ecosystem role and cultural significance. As part of an integrated undergraduate and graduate student training program in biodiversity and conservation genomics, the first reference genome for Juglans cinerea is described here. This chromosome-scale 539 Mb assembly was generated from over 100 × coverage of Oxford Nanopore long reads and scaffolded with the Juglans mandshurica genome. Scaffolding with a closely related species oriented and ordered the sequences in a manner more representative of the structure of the genome without altering the sequence. Comparisons with sequenced Juglandaceae revealed high levels of synteny and further supported J. cinerea's recent phylogenetic placement. Comparative assessment of gene family evolution revealed a significant number of contracting families, including several associated with biotic stress response.
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Affiliation(s)
- Cristopher R Guzman-Torres
- Department of Ecology and Evolutionary Biology, University of Connecticut, Storrs, CT 06269, USA
- Institute for Systems Genomics, University of Connecticut, Storrs, CT 06269, USA
| | - Emily Trybulec
- Institute for Systems Genomics, University of Connecticut, Storrs, CT 06269, USA
- Department of Molecular and Cell Biology, University of Connecticut, Storrs, CT 06269, USA
| | - Hannah LeVasseur
- Department of Ecology and Evolutionary Biology, University of Connecticut, Storrs, CT 06269, USA
- Institute for Systems Genomics, University of Connecticut, Storrs, CT 06269, USA
| | - Harshita Akella
- Department of Ecology and Evolutionary Biology, University of Connecticut, Storrs, CT 06269, USA
- Institute for Systems Genomics, University of Connecticut, Storrs, CT 06269, USA
| | - Maurice Amee
- Department of Ecology and Evolutionary Biology, University of Connecticut, Storrs, CT 06269, USA
- Institute for Systems Genomics, University of Connecticut, Storrs, CT 06269, USA
| | - Emily Strickland
- Department of Ecology and Evolutionary Biology, University of Connecticut, Storrs, CT 06269, USA
| | - Nicole Pauloski
- Institute for Systems Genomics, University of Connecticut, Storrs, CT 06269, USA
- Department of Molecular and Cell Biology, University of Connecticut, Storrs, CT 06269, USA
| | - Martin Williams
- Atlantic Forestry Center, Canadian Forest Service, Natural Resources Canada, Fredericton, NB E3B 5P7, Canada
| | | | - Sean Hoban
- The Center for Tree Science, The Morton Arboretum, Lisle, IL 60532, USA
| | - Keith Woeste
- USDA Forest Service, Northern Research Station, West Lafayette, IN 47906, USA
| | - Carolyn C Pike
- USDA Forest Service, Eastern Region State, Private and Tribal Forestry, West Lafayette, IN 47906, USA
| | - Karl C Fetter
- Department of Ecology and Evolutionary Biology, University of Connecticut, Storrs, CT 06269, USA
- Institute for Systems Genomics, University of Connecticut, Storrs, CT 06269, USA
| | - Cynthia N Webster
- Department of Ecology and Evolutionary Biology, University of Connecticut, Storrs, CT 06269, USA
- Institute for Systems Genomics, University of Connecticut, Storrs, CT 06269, USA
| | - Michelle L Neitzey
- Institute for Systems Genomics, University of Connecticut, Storrs, CT 06269, USA
- Department of Molecular and Cell Biology, University of Connecticut, Storrs, CT 06269, USA
| | - Rachel J O’Neill
- Institute for Systems Genomics, University of Connecticut, Storrs, CT 06269, USA
- Department of Molecular and Cell Biology, University of Connecticut, Storrs, CT 06269, USA
| | - Jill L Wegrzyn
- Department of Ecology and Evolutionary Biology, University of Connecticut, Storrs, CT 06269, USA
- Institute for Systems Genomics, University of Connecticut, Storrs, CT 06269, USA
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Steffen MM, Davis TW, McKay RML, Bullerjahn GS, Krausfeldt LE, Stough JMA, Neitzey ML, Gilbert NE, Boyer GL, Johengen TH, Gossiaux DC, Burtner AM, Palladino D, Rowe MD, Dick GJ, Meyer KA, Levy S, Boone BE, Stumpf RP, Wynne TT, Zimba PV, Gutierrez D, Wilhelm SW. Ecophysiological Examination of the Lake Erie Microcystis Bloom in 2014: Linkages between Biology and the Water Supply Shutdown of Toledo, OH. Environ Sci Technol 2017; 51:6745-6755. [PMID: 28535339 DOI: 10.1021/acs.est.7b00856] [Citation(s) in RCA: 107] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
Annual cyanobacterial blooms dominated by Microcystis have occurred in western Lake Erie (U.S./Canada) during summer months since 1995. The production of toxins by bloom-forming cyanobacteria can lead to drinking water crises, such as the one experienced by the city of Toledo in August of 2014, when the city was rendered without drinking water for >2 days. It is important to understand the conditions and environmental cues that were driving this specific bloom to provide a scientific framework for management of future bloom events. To this end, samples were collected and metatranscriptomes generated coincident with the collection of environmental metrics for eight sites located in the western basin of Lake Erie, including a station proximal to the water intake for the city of Toledo. These data were used to generate a basin-wide ecophysiological fingerprint of Lake Erie Microcystis populations in August 2014 for comparison to previous bloom communities. Our observations and analyses indicate that, at the time of sample collection, Microcystis populations were under dual nitrogen (N) and phosphorus (P) stress, as genes involved in scavenging of these nutrients were being actively transcribed. Targeted analysis of urea transport and hydrolysis suggests a potentially important role for exogenous urea as a nitrogen source during the 2014 event. Finally, simulation data suggest a wind event caused microcystin-rich water from Maumee Bay to be transported east along the southern shoreline past the Toledo water intake. Coupled with a significant cyanophage infection, these results reveal that a combination of biological and environmental factors led to the disruption of the Toledo water supply. This scenario was not atypical of reoccurring Lake Erie blooms and thus may reoccur in the future.
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Affiliation(s)
- Morgan M Steffen
- Department of Biology, James Madison University , Harrisonburg, Virginia 22807, United States
| | - Timothy W Davis
- NOAA-GLERL, 4840 South State Rd., Ann Arbor, Michigan 48108, United States
| | - R Michael L McKay
- Department of Biological Sciences, Bowling Green State University , Bowling Green, Ohio 43403, United States
| | - George S Bullerjahn
- Department of Biological Sciences, Bowling Green State University , Bowling Green, Ohio 43403, United States
| | - Lauren E Krausfeldt
- Department of Microbiology, University of Tennessee , Knoxville, Tennessee 37996, United States
| | - Joshua M A Stough
- Department of Microbiology, University of Tennessee , Knoxville, Tennessee 37996, United States
| | - Michelle L Neitzey
- Department of Biology, James Madison University , Harrisonburg, Virginia 22807, United States
| | - Naomi E Gilbert
- Department of Biology, James Madison University , Harrisonburg, Virginia 22807, United States
| | - Gregory L Boyer
- Department of Chemistry, State University of New York, Environmental Science and Forestry , Syracuse, New York 13210, United States
| | - Thomas H Johengen
- Cooperative Institute for Limnology and Ecosystems Research, University of Michigan , Ann Arbor, Michigan 48108, United States
| | - Duane C Gossiaux
- NOAA-GLERL, 4840 South State Rd., Ann Arbor, Michigan 48108, United States
| | - Ashley M Burtner
- Cooperative Institute for Limnology and Ecosystems Research, University of Michigan , Ann Arbor, Michigan 48108, United States
| | - Danna Palladino
- Cooperative Institute for Limnology and Ecosystems Research, University of Michigan , Ann Arbor, Michigan 48108, United States
| | - Mark D Rowe
- Cooperative Institute for Limnology and Ecosystems Research, University of Michigan , Ann Arbor, Michigan 48108, United States
| | - Gregory J Dick
- Department of Earth and Environmental Sciences, University of Michigan , Ann Arbor, Michigan 48109, United States
| | - Kevin A Meyer
- Department of Earth and Environmental Sciences, University of Michigan , Ann Arbor, Michigan 48109, United States
| | - Shawn Levy
- Genomic Service Laboratory, Hudson Alpha Institute for Biotechnology , Huntsville, Alabama 35806, United States
| | - Braden E Boone
- Genomic Service Laboratory, Hudson Alpha Institute for Biotechnology , Huntsville, Alabama 35806, United States
| | - Richard P Stumpf
- NOAA National Ocean Service, National Centers for Coastal Ocean Sciences, Silver Spring, Maryland 20910, United States
| | - Timothy T Wynne
- NOAA National Ocean Service, National Centers for Coastal Ocean Sciences, Silver Spring, Maryland 20910, United States
| | - Paul V Zimba
- Department of Life Sciences, Texas A&M Corpus Christi , Corpus Christi, Texas 78412, United States
| | - Danielle Gutierrez
- Department of Life Sciences, Texas A&M Corpus Christi , Corpus Christi, Texas 78412, United States
| | - Steven W Wilhelm
- Department of Microbiology, University of Tennessee , Knoxville, Tennessee 37996, United States
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