Evidence map›Paper›PMID 34833110›Full record

ArticleLife (Basel, Switzerland)2021

Comparative Genomics Analysis of Repetitive Elements in Ten Gymnosperm Species: "Dark Repeatome" and Its Abundance in Conifer and

Avi Titievsky, Yuliya A Putintseva, Elizaveta A Taranenko, Sofya Baskin, Natalia V Oreshkova, Elia Brodsky, Alexandra V Sharova, Vadim V Sharov, Julia Panov, Dmitry A Kuzmin and 2 more

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

Article in Life (Basel, Switzerland), 2021. 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
0.9field-weighted citation impact, top 19% 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, 5 citations in OpenAlex.

  1. Article
  2. A survey of k-mer methods and applications in bioinformatics.Computational and structural biotechnology journal · 2024
    Review
  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

12 authors at 5 institutions in 4 countries.

Avi TitievskyTauber Bioinformatics Research Center, University of Haifa, Haifa 3498838, Israel.
Yuliya A PutintsevaLaboratory of Forest Genomics, Genome Research and Education Center, Institute of Fundamental Biology and Biotechnology, Siberian Federal University, 660036 Krasnoyarsk, Russia.
Elizaveta A TaranenkoTauber Bioinformatics Research Center, University of Haifa, Haifa 3498838, Israel.
Sofya BaskinTauber Bioinformatics Research Center, University of Haifa, Haifa 3498838, Israel.
Natalia V OreshkovaLaboratory of Forest Genomics, Genome Research and Education Center, Institute of Fundamental Biology and Biotechnology, Siberian Federal University, 660036 Krasnoyarsk, Russia.
Elia BrodskyPine Biotech Inc., New Orleans, LA 70112, USA.ORCID 0000-0003-3068-416X
Alexandra V SharovaTauber Bioinformatics Research Center, University of Haifa, Haifa 3498838, Israel.
Vadim V SharovTauber Bioinformatics Research Center, University of Haifa, Haifa 3498838, Israel.
Julia PanovTauber Bioinformatics Research Center, University of Haifa, Haifa 3498838, Israel.ORCID 0000-0003-2392-4073
Dmitry A KuzminDepartment of High Performance Computing, Institute of Space and Information Technologies, Siberian Federal University, 660074 Krasnoyarsk, Russia.
Leonid BrodskyTauber Bioinformatics Research Center, University of Haifa, Haifa 3498838, Israel.
Konstantin V KrutovskyLaboratory of Forest Genomics, Genome Research and Education Center, Institute of Fundamental Biology and Biotechnology, Siberian Federal University, 660036 Krasnoyarsk, Russia.ORCID 0000-0002-8819-7084
Siberian Federal University · RUUniversity of Haifa · ILKrasnoyarsk Scientific Center · RUCook Biotech (United States) · USVoronezh State University of Forestry and Technologies · RU

Funding

Government of the Russian Federation 14.Y26.31.0004Laszlo N. Tauber Family Foundation XXX
6 · The paper itself

Abstract

Repetitive elements (RE) and transposons (TE) can comprise up to 80% of some plant genomes and may be essential for regulating their evolution and adaptation. The "repeatome" information is often unavailable in assembled genomes because genomic areas of repeats are challenging to assemble and are often missing from final assembly. However, raw genomic sequencing data contain rich information about RE/TEs. Here, raw genomic NGS reads of 10 gymnosperm species were studied for the content and abundance patterns of their "repeatome". We utilized a combination of alignment on databases of repetitive elements and de novo assembly of highly repetitive sequences from genomic sequencing reads to characterize and calculate the abundance of known and putative repetitive elements in the genomes of 10 conifer plants:

Indexed as

gymnospermsprincipal component analysisrepetitive elements

Identifiers

PMID34833110
PMCPMC8620675
OpenAlexW3213259375

What OpenQuestion holds

Textmetadata
LicenceCC BY
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.