Evidence map›Paper›PMID 41928370›Full record

ArticleThe New phytologist2026

Structure and sequence evolution in the pennycress (Thlaspi arvense) pangenome.

Kevin A Bird, Joanna L Rifkin, Chloee M McLaughlin, Avril M Harder, Pawan Basnet, Ella Katz, Tomáš Brůna, Kerrie Barry, LoriBeth Boston, Christopher Daum and 16 more

Abstract read
PubMed Full text at PMC Publisher
In one paragraph

Article in The New phytologist, 2026. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 1 paper.

0numbers the graph read from it
0cells of the map it votes in
1citing papers in PubMed
–field-weighted citation impact
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

1 citing paper in PubMed.

  1. Article
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

26 authors.

Kevin A Bird *Department of Trait Diversity and Function, Royal Botanic Gardens, Kew, Richmond, Surrey, TW9 3AE, UK.ORCID https://orcid.org/0000-0002-3174-3646
Joanna L Rifkin *HudsonAlpha Institute for Biotechnology, Huntsville, AL, 35806, USA.ORCID https://orcid.org/0000-0003-1980-5557
Chloee M McLaughlinHudsonAlpha Institute for Biotechnology, Huntsville, AL, 35806, USA.ORCID https://orcid.org/0000-0002-6345-6764
Avril M HarderHudsonAlpha Institute for Biotechnology, Huntsville, AL, 35806, USA.ORCID https://orcid.org/0000-0001-7371-4002
Pawan BasnetDepartment of Plant and Agroecosystem Sciences, University of Wisconsin, Madison, Madison, WI, 53706, USA.ORCID https://orcid.org/0000-0001-5496-9165
Ella KatzDepartment of Plant Sciences, University of California at Davis, Davis, CA, 95616, USA.ORCID https://orcid.org/0000-0003-1619-5597
Tomáš BrůnaUS Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA.ORCID https://orcid.org/0000-0001-9811-5532
Kerrie BarryUS Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA.ORCID https://orcid.org/0000-0002-8999-6785
LoriBeth BostonHudsonAlpha Institute for Biotechnology, Huntsville, AL, 35806, USA.
Christopher DaumUS Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA.
Jie GuoUS Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA.
Anna LipzenUS Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA.ORCID https://orcid.org/0000-0003-2293-9329
Christopher PlottHudsonAlpha Institute for Biotechnology, Huntsville, AL, 35806, USA.ORCID https://orcid.org/0000-0002-0109-5174
Jerry W JenkinsHudsonAlpha Institute for Biotechnology, Huntsville, AL, 35806, USA.ORCID https://orcid.org/0000-0002-7943-3997
Rachel WalsteadHudsonAlpha Institute for Biotechnology, Huntsville, AL, 35806, USA.ORCID https://orcid.org/0000-0002-4372-2703
Shanmugam RajasekarArizona Genomics Institute, University of Arizona, Tucson, AZ, 85721, USA.
Jayson TalagArizona Genomics Institute, University of Arizona, Tucson, AZ, 85721, USA.
Katherine FrelsDepartment of Agronomy and Horticulture, University of Nebraska, Lincoln, NE, 68583, USA.
Kathleen GreenhamDepartment of Plant and Microbial Biology, University of Minnesota, St. Paul, MN, 55108, USA.ORCID https://orcid.org/0000-0001-7681-5263
Shelby EllisonDepartment of Plant and Agroecosystem Sciences, University of Wisconsin, Madison, Madison, WI, 53706, USA.ORCID https://orcid.org/0000-0002-0790-4286
Jane GrimwoodHudsonAlpha Institute for Biotechnology, Huntsville, AL, 35806, USA.ORCID https://orcid.org/0000-0002-8356-8325
Jeremy SchmutzHudsonAlpha Institute for Biotechnology, Huntsville, AL, 35806, USA.ORCID https://orcid.org/0000-0001-8062-9172
Patrick P EdgerDepartment of Horticulture, MI State University, East Lansing, MI, 48824, USA.ORCID https://orcid.org/0000-0001-6836-3041
J Chris PiresDepartment of Soil and Crop Sciences, CO State University, Fort Collins, CO, 80523, USA.ORCID https://orcid.org/0000-0001-9682-2639
John T LovellHudsonAlpha Institute for Biotechnology, Huntsville, AL, 35806, USA.ORCID https://orcid.org/0000-0002-8938-1166
Daniel J KliebensteinDepartment of Plant Sciences, University of California at Davis, Davis, CA, 95616, USA.ORCID https://orcid.org/0000-0001-5759-3175

Funding

Division of Integrative Organismal Systems 2208944Division of Molecular & Cellular Biosciences 1906486Joint Genome Institute 10.46936/10.25585/60001293National Institute of Food and Agriculture 2019-05709
6 · The paper itself

Abstract

Eukaryotic genomes harbor many forms of variation, including nucleotide diversity and structural polymorphisms, which experience natural selection and contribute to genome evolution and biodiversity. Harnessing this variation for agriculture hinges on our ability to detect, quantify, catalog, and deploy genetic diversity. Here, we explore seven complete genomes of the emerging biofuel crop pennycress (Thlaspi arvense) drawn from across the species' current genetic diversity to catalog variation in genome structure and content. Across this new pangenome resource, we find contrasting evolutionary modes in different genomic zones. Gene-poor, repeat-rich pericentromeric regions experience frequent rearrangements, including repeated centromere repositioning. By contrast, conserved gene-dense chromosome arms maintain large-scale synteny across accessions even in fast-evolving NOD-like receptor immune genes, where microsynteny breaks down across species, but gene cluster positioning macrosynteny is maintained. Our findings highlight that multiple elements of the genome experience dynamic evolution that conserves functional content on the chromosome scale but allows repositioning and presence-absence variation on a local scale. This diversity is invisible to classical reference-based strategies and highlights the strength and utility of pangenomic resources. These results provide a valuable case study of rapid genomic structural evolution within a species and powerful resources for crop development in an emerging biofuel crop.

Indexed as

Evolution, MolecularGenome, PlantThlaspiCentromereChromosomes, PlantGenes, PlantGenetic VariationSyntenycentromerePangenomeresistance genesstructural variationThlaspi arvense

Identifiers

PMID41928370
PMCPMC13150303

What Socratic 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 Socratic graph.