Evidence map›Paper›PMID 32050897›Full record

ArticleBMC genomics2020

Pan-tissue transcriptome analysis of long noncoding RNAs in the American beaver Castor canadensis.

Amita Kashyap, Adelaide Rhodes, Brent Kronmiller, Josie Berger, Ashley Champagne, Edward W Davis, Mitchell V Finnegan, Matthew Geniza, David A Hendrix, Christiane V Löhr and 7 more

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

Article in BMC genomics, 2020. 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
0.6field-weighted citation impact, top 42% 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, 8 citations in OpenAlex.

  1. Article
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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

17 authors at 2 institutions in 1 country.

Amita KashyapDepartment of Biomedical Sciences, Oregon State University, Corvallis, OR, USA.
Adelaide RhodesCenter for Genome Research and Biocomputing, Oregon State University, Corvallis, OR, USA.
Brent KronmillerCenter for Genome Research and Biocomputing, Oregon State University, Corvallis, OR, USA.
Josie BergerCollege of Forestry, Oregon State University, Corvallis, OR, USA.
Ashley ChampagneCollege of Forestry, Oregon State University, Corvallis, OR, USA.
Edward W DavisCenter for Genome Research and Biocomputing, Oregon State University, Corvallis, OR, USA.
Mitchell V FinneganOregon Zoo, Portland, OR, USA.
Matthew GenizaDepartment of Botany and Plant Pathology, Oregon State University, Corvallis, OR, USA.
David A HendrixDepartment of Biochemistry and Biophysics, Oregon State University, Corvallis, OR, USA.
Christiane V LöhrDepartment of Biomedical Sciences, Oregon State University, Corvallis, OR, USA.
Vanessa M PetroCollege of Forestry, Oregon State University, Corvallis, OR, USA.
Thomas J SharptonDepartment of Microbiology, Oregon State University, Corvallis, OR, USA.
Jackson WellsCenter for Genome Research and Biocomputing, Oregon State University, Corvallis, OR, USA.
Clinton W EppsDepartment of Fisheries and Wildlife, Oregon State University, Corvallis, OR, USA.
Pankaj JaiswalDepartment of Botany and Plant Pathology, Oregon State University, Corvallis, OR, USA.
Brett M TylerCenter for Genome Research and Biocomputing, Oregon State University, Corvallis, OR, USA.
Stephen A RamseyDepartment of Biomedical Sciences, Oregon State University, Corvallis, OR, USA. stephen.ramsey@oregonstate.edu.ORCID http://orcid.org/0000-0002-2168-5403
Oregon State University · USOregon Zoo · US

Funding

No grant is acknowledged in the PubMed record.

6 · The paper itself

Abstract

backgroundLong noncoding RNAs (lncRNAs) have roles in gene regulation, epigenetics, and molecular scaffolding and it is hypothesized that they underlie some mammalian evolutionary adaptations. However, for many mammalian species, the absence of a genome assembly precludes the comprehensive identification of lncRNAs. The genome of the American beaver (Castor canadensis) has recently been sequenced, setting the stage for the systematic identification of beaver lncRNAs and the characterization of their expression in various tissues. The objective of this study was to discover and profile polyadenylated lncRNAs in the beaver using high-throughput short-read sequencing of RNA from sixteen beaver tissues and to annotate the resulting lncRNAs based on their potential for orthology with known lncRNAs in other species.

resultsUsing de novo transcriptome assembly, we found 9528 potential lncRNA contigs and 187 high-confidence lncRNA contigs. Of the high-confidence lncRNA contigs, 147 have no known orthologs (and thus are putative novel lncRNAs) and 40 have mammalian orthologs. The novel lncRNAs mapped to the Oregon State University (OSU) reference beaver genome with greater than 90% sequence identity. While the novel lncRNAs were on average shorter than their annotated counterparts, they were similar to the annotated lncRNAs in terms of the relationships between contig length and minimum free energy (MFE) and between coverage and contig length. We identified beaver orthologs of known lncRNAs such as XIST, MEG3, TINCR, and NIPBL-DT. We profiled the expression of the 187 high-confidence lncRNAs across 16 beaver tissues (whole blood, brain, lung, liver, heart, stomach, intestine, skeletal muscle, kidney, spleen, ovary, placenta, castor gland, tail, toe-webbing, and tongue) and identified both tissue-specific and ubiquitous lncRNAs.

conclusionsTo our knowledge this is the first report of systematic identification of lncRNAs and their expression atlas in beaver. LncRNAs-both novel and those with known orthologs-are expressed in each of the beaver tissues that we analyzed. For some beaver lncRNAs with known orthologs, the tissue-specific expression patterns were phylogenetically conserved. The lncRNA sequence data files and raw sequence files are available via the web supplement and the NCBI Sequence Read Archive, respectively.

Indexed as

Gene Expression ProfilingRNA, Long NoncodingTranscriptomeAnimalsComputational BiologyGene Expression RegulationGenomeMolecular Sequence AnnotationNucleic Acid ConformationOrgan SpecificityRodentiaRNA, Long NoncodingBeaverCastor canadensisExpression atlaslncRNALong noncoding RNATranscriptome

Identifiers

PMID32050897
PMCPMC7014947
OpenAlexW3007454736

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.