Evidence map›Paper›PMID 35809222›Full record

ArticleThe Journal of heredity2022

Reference Genome of the Black Surfperch, Embiotoca jacksoni (Embiotocidae, Perciformes), a California Kelp Forest Fish That Lacks a Pelagic Larval Stage.

Giacomo Bernardi, Jason A Toy, Merly Escalona, Mohan P A Marimuthu, Ruta Sahasrabudhe, Oanh Nguyen, Samuel Sacco, Eric Beraut, Erin Toffelmier, Courtney Miller and 1 more

Abstract read
PubMed Full text at PMC Publisher
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 3 papers.

0numbers the graph read from it
0cells of the map it votes in
3citing 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

3 citing papers in PubMed.

  1. Article
  2. Article
  3. 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

11 authors.

Giacomo BernardiDepartment of Ecology and Evolutionary Biology, University of California-Santa Cruz, Santa Cruz, CA, USA.ORCID 0000-0001-8630-6657
Jason A ToyDepartment of Ecology and Evolutionary Biology, University of California-Santa Cruz, Santa Cruz, CA, USA.ORCID 0000-0002-2126-7826
Merly EscalonaDepartment of Biomolecular Engineering, University of California-Santa Cruz, Santa Cruz, CA, USA.ORCID 0000-0003-0213-4777
Mohan P A MarimuthuDNA Technologies and Expression Analysis Core Laboratory, Genome Center, University of California-Davis, Davis, CA, USA.ORCID 0000-0001-6121-3286
Ruta SahasrabudheDNA Technologies and Expression Analysis Core Laboratory, Genome Center, University of California-Davis, Davis, CA, USA.
Oanh NguyenDNA Technologies and Expression Analysis Core Laboratory, Genome Center, University of California-Davis, Davis, CA, USA.
Samuel SaccoDepartment of Ecology and Evolutionary Biology, University of California-Santa Cruz, Santa Cruz, CA, USA.
Eric BerautDepartment of Ecology and Evolutionary Biology, University of California-Santa Cruz, Santa Cruz, CA, USA.
Erin ToffelmierDepartment of Ecology and Evolutionary Biology, University of California-Los Angeles, Los Angeles, CA, USA.
Courtney MillerDepartment of Ecology and Evolutionary Biology, University of California-Los Angeles, Los Angeles, CA, USA.
H Bradley ShafferDepartment of Ecology and Evolutionary Biology, University of California-Los Angeles, Los Angeles, CA, USA.ORCID 0000-0002-5795-9242

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

Surfperches (Family Embiotocidae) are viviparous temperate reef fishes that brood their young. This life history trait translates into limited dispersal, strong population structure, and an unusually strong potential for local adaptation in a marine fish. As part of the California Conservation Genomics Project (CCGP), we sequenced the genome of the Black Surfperch, Embiotoca jacksoni, to establish a genomic model for understanding phylogeographic patterns of marine organisms in California. These patterns, in turn, may inform the design of marine protected areas using dispersal models based on genomic data. The genome of E. jacksoni is typical of marine fishes at less than 1Gb (genome size = 635 Mb), and our assembly is near-chromosome level (contig N50 = 6.5Mb, scaffold N50 = 15.5 Mb, BUSCO = 98.1%). Within the context of the CCGP, the genome will be used as a reference for future whole genome resequencing projects aimed at enhancing our knowledge of the population structure of the species, and efficacy of Marine Protected Areas across the state.

Indexed as

KelpPerciformesAnimalsFishesForestsLarvaCalifornia Conservation Genomics ProjectCCGPMarine Protected Areas

Identifiers

PMID35809222
PMCPMC9709976

What OpenQuestion holds

Textmetadata
LicenceCC BY-NC
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.