Evidence map›Paper›PMID 37703053›Full record

ArticleG3 (Bethesda, Md.)2024

Conserving a threatened North American walnut: a chromosome-scale reference genome for butternut (Juglans cinerea).

Cristopher R Guzman-Torres, Emily Trybulec, Hannah LeVasseur, Harshita Akella, Maurice Amee, Emily Strickland, Nicole Pauloski, Martin Williams, Jeanne Romero-Severson, Sean Hoban and 7 more

Open access · goldAbstract read
PubMed Full text at PMC Publisher
In one paragraph

Article in G3 (Bethesda, Md.), 2024. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 5 papers.

0numbers the graph read from it
0cells of the map it votes in
5citing papers in PubMed
3.3field-weighted citation impact, top 8% of its field
1 · What the graph read from it

What it found

Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.

The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.

2 · The registry

The trial behind it

Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.

Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.

3 · Its place in the literature

Who cites it

5 citing papers in PubMed, 11 citations in OpenAlex.

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4 · The record

Corrections and comments

PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.

5 · Who and what money

Authors and funding

17 authors at 7 institutions in 2 countries.

Cristopher R Guzman-TorresDepartment of Ecology and Evolutionary Biology, University of Connecticut, Storrs, CT 06269, USA.
Emily TrybulecInstitute for Systems Genomics, University of Connecticut, Storrs, CT 06269, USA.
Hannah LeVasseurDepartment of Ecology and Evolutionary Biology, University of Connecticut, Storrs, CT 06269, USA.
Harshita AkellaDepartment of Ecology and Evolutionary Biology, University of Connecticut, Storrs, CT 06269, USA.
Maurice AmeeDepartment of Ecology and Evolutionary Biology, University of Connecticut, Storrs, CT 06269, USA.
Emily StricklandDepartment of Ecology and Evolutionary Biology, University of Connecticut, Storrs, CT 06269, USA.
Nicole PauloskiInstitute for Systems Genomics, University of Connecticut, Storrs, CT 06269, USA.
Martin WilliamsAtlantic Forestry Center, Canadian Forest Service, Natural Resources Canada, Fredericton, NB E3B 5P7, Canada.
Jeanne Romero-SeversonDepartment of Biological Sciences, University of Notre Dame, Notre Dame, IN 46556, USA.
Sean HobanThe Center for Tree Science, The Morton Arboretum, Lisle, IL 60532, USA.
Keith WoesteUSDA Forest Service, Northern Research Station, West Lafayette, IN 47906, USA.
Carolyn C PikeUSDA Forest Service, Eastern Region State, Private and Tribal Forestry, West Lafayette, IN 47906, USA.
Karl C FetterDepartment of Ecology and Evolutionary Biology, University of Connecticut, Storrs, CT 06269, USA.
Cynthia N WebsterDepartment of Ecology and Evolutionary Biology, University of Connecticut, Storrs, CT 06269, USA.
Michelle L NeitzeyInstitute for Systems Genomics, University of Connecticut, Storrs, CT 06269, USA.
Rachel J O'NeillInstitute for Systems Genomics, University of Connecticut, Storrs, CT 06269, USA.
Jill L WegrzynDepartment of Ecology and Evolutionary Biology, University of Connecticut, Storrs, CT 06269, USA.
Institute for Systems Biology · USUniversity of Connecticut · USMorton Arboretum · USNatural Resources Canada · CANorthern Research Station · USUniversity of Notre Dame · USUS Forest Service · US

Funding

No grant is acknowledged in the PubMed record.

6 · The paper itself

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.

Indexed as

JuglansChromosomesEcosystemHumansNorth AmericaPhylogenyUnited Statesbutternutconservation geneticsgenome annotationgenome evolutionJuglandaceaelong-readmethylationnanoporephylogenyreference genome

Identifiers

PMID37703053
PMCPMC10849370
OpenAlexW4386704814

What OpenQuestion holds

Textmetadata
LicenceCC BY
Read underepoch 390

Registered trials

None linked

Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.