ConTEdb: a comprehensive database of transposable elements in conifers.

Fei Yi, Juanjuan Ling, Yao Xiao, Hanguo Zhang, Fangqun Ouyang, Junhui Wang

Open access · goldAbstract readDataset

In one paragraph

Article in Database : the journal of biological databases and curation, 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 9 papers.

0numbers the graph read from it

0cells of the map it votes in

9citing papers in PubMed

3.0field-weighted citation impact, top 8% 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

9 citing papers in PubMed, 18 citations in OpenAlex.

PlantLTRdb: An interactive database for 195 plant species LTR-retrotransposons.Frontiers in plant science · 2023
Article
Evaluating the accuracy of variant calling methods using the frequency of parent-offspring genotype mismatch.Molecular ecology resources · 2022
Article
TransposonUltimate: software for transposon classification, annotation and detection.Nucleic acids research · 2022
Article
CicerSpTEdb: A web-based database for high-resolution genome-wide identification of transposable elements in Cicer species.PloS one · 2021
Article
Mobile genomics: tools and techniques for tackling transposons.Philosophical transactions of the Royal Society of London. Series B, Biological sciences · 2020
Review
Identification of Transposable Elements in Conifer and Their Potential Application in Breeding.Evolutionary bioinformatics online · 2020
Article
DeviaTE: Assembly-free analysis and visualization of mobile genetic element composition.Molecular ecology resources · 2019
Article
Novel Insights into Plant Genome Evolution and Adaptation as Revealed through Transposable Elements and Non-Coding RNAs in Conifers.Genes · 2019
Review
PICEAdatabase: a web database for Picea omics and phenotypic information.Database : the journal of biological databases and curation · 2019
Article

4 · The record

Corrections and comments

Commented on by
Identification of Transposable Elements in Conifer and Their Potential Application in Breeding.2020

5 · Who and what money

Authors and funding

6 authors at 3 institutions in 1 country.

Fei YiState Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Tree Breeding and Cultivation of State Forestry Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, China.

Juanjuan LingState Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Tree Breeding and Cultivation of State Forestry Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, China.

Yao XiaoState Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Tree Breeding and Cultivation of State Forestry Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, China.

Hanguo ZhangState Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin, China.

Fangqun OuyangState Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Tree Breeding and Cultivation of State Forestry Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, China.

Junhui WangState Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Tree Breeding and Cultivation of State Forestry Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, China.

Chinese Academy of Forestry · CNChina Three Gorges University · CNNortheast Forestry University · CN

Funding

No grant is acknowledged in the PubMed record.

6 · The paper itself

Abstract

Conifers are the largest and most ubiquitous group of gymnosperms and have significant ecological significance and economic importance. However, the huge and complex genomes have hindered the sequencing and mining of conifer genomes. In this study, we identified 413 423 transposable elements (TEs) from Picea abies, Picea glauca and Pinus taeda using a combination of multiple approaches and classified them into 11 133 families. A comprehensive web-based database, ConTEdb, was constructed and served for researchers. ConTEdb enables users to browse, retrieve and download the TE sequences from the database. Several analysis tools are integrated into ConTEdb to help users mine the TE data easily and effectively. In summary, ConTEdb provides a platform to study TE biology and functional genomics in conifers.

Indexed as

Databases, GeneticGenes, PlantInternetSoftwareTracheophyta

Identifiers

PMID30576494

DOI10.1093/database/bay131

PMCPMC6301336

OpenAlexW2912411511

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.