Evidence map›Paper›PMID 37149716›Full record

ArticleEvoDevo2023

Transcriptomic analysis of cave, surface, and hybrid samples of the isopod Asellus aquaticus and identification of chromosomal location of candidate genes for cave phenotype evolution.

Haeli J Lomheim, Lizet Reyes Rodas, Lubna Mulla, Layla Freeborn, Dennis A Sun, Sheri A Sanders, Meredith E Protas

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

Article in EvoDevo, 2023. 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
3.2field-weighted citation impact, top 10% 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

3 citing papers in PubMed, 4 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

7 authors at 4 institutions in 1 country.

Haeli J LomheimDepartment of Natural Sciences and Mathematics, Dominican University of California, San Rafael, CA, 94901, USA.
Lizet Reyes RodasDepartment of Natural Sciences and Mathematics, Dominican University of California, San Rafael, CA, 94901, USA.
Lubna MullaDepartment of Natural Sciences and Mathematics, Dominican University of California, San Rafael, CA, 94901, USA.
Layla FreebornCenter for Research Data and Digital Scholarship, University of Colorado Boulder, Boulder, CO, 80309, USA.
Dennis A SunDepartment of Molecular and Cell Biology, University of California at Berkeley, Berkeley, CA, 94720, USA.
Sheri A SandersDepartment of Biological Sciences, University of Notre Dame, Notre Dame, IN, 46556, USA.
Meredith E ProtasDepartment of Natural Sciences and Mathematics, Dominican University of California, San Rafael, CA, 94901, USA. meredith.protas@dominican.edu.
Dominican University of California · USUniversity of California, Berkeley · USUniversity of Colorado Boulder · USUniversity of Notre Dame · US

Funding

Genetic and functional analysis of eye degeneration in natural populations of a cave-dwelling crustaceanR15EY029499 · NEI · DOMINICAN UNIVERSITY · PI PROTAS, MEREDITH E · 2019 to 2024
$640k
NEI NIH HHS R15 EY029499NEI NIH HHS R15EY029499
6 · The paper itself

Abstract

backgroundTranscriptomic methods can be used to elucidate genes and pathways responsible for phenotypic differences between populations. Asellus aquaticus is a freshwater isopod crustacean with surface- and cave-dwelling ecomorphs that differ greatly in multiple phenotypes including pigmentation and eye size. Multiple genetic resources have been generated for this species, but the genes and pathways responsible for cave-specific characteristics have not yet been identified. Our goal was to generate transcriptomic resources in tandem with taking advantage of the species' ability to interbreed and generate hybrid individuals.

resultsWe generated transcriptomes of the Rakov Škocjan surface population and the Rak Channel of Planina Cave population that combined Illumina short-read assemblies and PacBio Iso-seq long-read sequences. We investigated differential expression at two different embryonic time points as well as allele-specific expression of F

conclusionsAs expected, genes involved in phototransduction and ommochrome synthesis were under-expressed in the cave samples as compared to the surface samples. Allele-specific expression analysis of F

Indexed as

Allele-specific expressionCaveEyePigmentTroglomorphy

Identifiers

PMID37149716
PMCPMC10163715
OpenAlexW4372357461

What OpenQuestion holds

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LicenceCC BY
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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.