Evidence map›Paper›PMID 36107789›Full record

ArticleThe Journal of heredity2022

Reference genome of the color polymorphic desert annual plant sandblossoms, Linanthus parryae.

Ioana G Anghel, Sarah J Jacobs, Merly Escalona, Mohan P A Marimuthu, Colin W Fairbairn, Eric Beraut, Oanh Nguyen, Erin Toffelmier, H Bradley Shaffer, Felipe Zapata

Abstract read
In one paragraph

Article in The Journal of heredity, 2022. 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
–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

5 citing papers in PubMed.

  1. Article
  2. Article
  3. Article
  4. Article
  5. Review
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

10 authors.

Ioana G AnghelDepartment of Ecology and Evolutionary Biology, University of California, Los Angeles, Los Angeles, CA, United States.ORCID 0000-0002-1454-8718
Sarah J JacobsDepartment of Botany, California Academy of Sciences, San Francisco, CA, United States.ORCID 0000-0002-3125-6266
Merly EscalonaDepartment of Biomolecular Engineering, University of California Santa Cruz, Santa Cruz, CA, United States.ORCID 0000-0003-0213-4777
Mohan P A MarimuthuDNA Technologies and Expression Analysis Core Laboratory, Genome Center, University of California-Davis, Davis, CA, United States.ORCID 0000-0001-6121-3286
Colin W FairbairnDepartment of Ecology and Evolutionary Biology, University of California, Santa Cruz, Santa Cruz, CA, United States.
Eric BerautDepartment of Ecology and Evolutionary Biology, University of California, Santa Cruz, Santa Cruz, CA, United States.ORCID 0000-0002-4443-6282
Oanh NguyenDNA Technologies and Expression Analysis Core Laboratory, Genome Center, University of California-Davis, Davis, CA, United States.ORCID 0000-0003-1492-2084
Erin ToffelmierDepartment of Ecology and Evolutionary Biology, University of California, Los Angeles, Los Angeles, CA, United States.ORCID 0000-0001-6028-8497
H Bradley ShafferDepartment of Ecology and Evolutionary Biology, University of California, Los Angeles, Los Angeles, CA, United States.ORCID 0000-0002-5795-9242
Felipe ZapataDepartment of Ecology and Evolutionary Biology, University of California, Los Angeles, Los Angeles, CA, United States.ORCID 0000-0002-9386-0573

Funding

Pacific Biosciences PacBio RS Single Molecule Real Time SequencerS10OD018174 · OD · UNIVERSITY OF CALIFORNIA BERKELEY · PI ROKHSAR, DANIEL SOLEYMAN · 2014 to 2014
$600k
Acquisition of Covaris E220 and Sciclone G3 systems for high throughput sequencinS10OD010786 · OD · UNIVERSITY OF CALIFORNIA AT DAVIS · PI COMAI, LUCA · 2012 to 2012
$311k
NIH HHS 1S10OD010786-01NIH HHS S10 OD010786NIH HHS S10 OD018174
6 · The paper itself

Abstract

Sandblossoms, Linanthus parryae is a widespread annual plant species found in washes and sandy open habitats across the Mojave Desert and Eastern Sierra Nevada of California. Studies in this species have played a central role in evolutionary biology, serving as the first test cases of the shifting balance theory of evolution, models of isolation by distance, and metrics to describe the genetic structure of natural populations. Despite the importance of L. parryae in the development of landscape genetics and phylogeography, there are no genomic resources available for the species. Through the California Conservation Genomics Project, we assembled the first genome in the genus Linanthus. Using PacBio HiFi long reads and Hi-C chromatin conformation capture, we assembled 123 scaffolds spanning 1.51 Gb of the 1.96 Gb estimated genome, with a contig N50 of 18.7 Mb and a scaffold N50 of 124.8 Mb. This assembly, with a BUSCO completeness score of 88.7%, will allow us to revisit foundational ideas central to our understanding of how evolutionary forces operate in a geographic landscape. In addition, it will be a new resource to uncover adaptations to arid environments in the fragile desert habitat threatened by urban and solar farm development, climate change, and off-road vehicles.

Indexed as

Adaptation, PhysiologicalGenomeChromosomesGenomicsCalifornia Conservation Genomics ProjectCCGPdesert plantPolemoniaceaepolymorphism

Identifiers

PMID36107789
PMCPMC9709995

What OpenQuestion holds

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LicenceCC BY
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 OpenQuestion graph.