Evidence map›Paper›PMID 41615023›Full record

ArticleThe Journal of heredity2026

Chromosome-level reference genome of a foundational California native legume, Acmispon strigosus.

Lorena Torres Martínez, Merly Escalona, Erin Toffelmier, Courtney Miller, Ruta Sahasrahbudhe, Mohan P A Marimuthu, Oanh Nguyen, Noravit Chumchim, Eric Beraut, Samuel Sacco and 6 more

Abstract read
PubMed Full text at PMC Publisher
In one paragraph

Article in The Journal of heredity, 2026. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Not yet cited in PubMed.

0numbers the graph read from it
0cells of the map it votes in
0citing 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

0 citing papers in PubMed.

No citing paper in PubMed yet.

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

16 authors.

Lorena Torres MartínezDepartment of Evolution, Ecology, and Organismal Biology, University of California, Riverside, CA, United States.ORCID 0000-0002-0903-8633
Merly EscalonaDepartment of Biomolecular Engineering, University of California, Santa Cruz, CA, United States.
Erin ToffelmierDepartment of Ecology and Evolutionary Biology, University of California, Los Angeles, CA, United States.ORCID 0000-0001-6028-8497
Courtney MillerDepartment of Ecology and Evolutionary Biology, University of California, Los Angeles, CA, United States.
Ruta SahasrahbudheDNA Technologies and Expression Analysis Core Laboratory, Genome Center, University of California, Davis, CA, United States.
Mohan P A MarimuthuDNA Technologies and Expression Analysis Core Laboratory, Genome Center, University of California, Davis, CA, United States.
Oanh NguyenDNA Technologies and Expression Analysis Core Laboratory, Genome Center, University of California, Davis, CA, United States.
Noravit ChumchimDNA Technologies and Expression Analysis Core Laboratory, Genome Center, University of California, Davis, CA, United States.
Eric BerautDepartment of Ecology and Evolutionary Biology, University of California, Santa Cruz, CA, United States.
Samuel SaccoDepartment of Ecology and Evolutionary Biology, University of California, Santa Cruz, CA, United States.
William SeligmannDepartment of Biomolecular Engineering, University of California, Santa Cruz, CA, United States.
Colin W FairbairnDepartment of Ecology and Evolutionary Biology, University of California, Santa Cruz, CA, United States.
Robert D CooperDepartment of Fish and Wildlife Conservation, Virginia Polytechnic Institute and State University, Blacksburg, VA, United States.
H Bradley ShafferDepartment of Ecology and Evolutionary Biology, University of California, Los Angeles, CA, United States.
Jessica PurcellDepartment of Entomology, University of California, Riverside, CA, United States.
Joel L SachsDepartment of Evolution, Ecology, and Organismal Biology, University of California, Riverside, CA, United States.ORCID 0000-0002-0221-9247

Funding

California Conservation Genomics ProjectUniversity of California by the State of California, State Budget Act of 2019 RSI-19-690224
6 · The paper itself

Abstract

Acmispon is a legume genus that has diversified within the California Floristic Province. Acmispon species live in a variety of habitats, including coastal sage scrub, deserts, grasslands, and woodlands, and form symbiotic associations with nitrogen-fixing bacteria. Here, we report the first chromosome-level assembly of Acmispon strigosus (strigose bird's-foot trefoil or strigose lotus) as part of the California Conservation Genomics Project. Consistent with the reference genome pipelines of the California Conservation Genomics Project, we used Pacific Biosciences HiFi long reads and Hi-C chromatin-proximity sequencing technology to produce a de novo assembled genome. The assembly is 519 Mb in length, with a contig N50 of 22.97 Mb, scaffolded into seven pseudochromosomes. Using the NCBI EGAPx pipeline, we annotated a total of 21,347 genes resulting in a protein Benchmarking Universal Single-Copy Orthologs (BUSCO) completeness score of 91.5%. This is the first genome assembled for Acmispon and among the first genomic resources available for a native California legume. The assembly BUSCO completeness score of 94.8% makes it one of the most complete genomes for the tribe Loteae (Fabaceae). Generating whole-genome sequences will contribute to our general understanding of nitrogen-fixing legume's adaptations to diverse soil and environmental conditions, interactions with nitrogen fixing Bradyrhizobium and Mesorhizobium symbionts, and the degrading effects of pollution-induced nitrogen deposition on the legume-rhizobium symbiosis in California. These data will also help to reconstruct phylogenetic relationships among Acmispon spp., which remain unresolved.

Indexed as

Chromosomes, PlantFabaceaeGenome, PlantCaliforniaGenomicsMolecular Sequence AnnotationPhylogenySequence Analysis, DNASymbiosisbiological nitrogen fixationCalifornia conservation genomics projectlegumeLoteaerhizobiasymbiosis

Identifiers

PMID41615023
PMCPMC13326405

What Socratic holds

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LicenceCC BY-NC
Read underepoch 390

Registered trials

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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.