ArticleGenome biology2004
Insertion bias and purifying selection of retrotransposons in the Arabidopsis thaliana genome.
Article in Genome biology, 2004. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 88 papers.
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.
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.
Who cites it
88 citing papers in PubMed, 163 citations in OpenAlex.
- Differential LTR-retrotransposon dynamics across polyploidization, speciation, domestication, and improvement of cotton (Gossypium).Genome biology · 2025Article
- Structural and Evolutionary Analysis ofInternational journal of molecular sciences · 2025Article
- Deciphering octoploid strawberry evolution with serial LTR similarity matrices for subgenome partition.Horticulture research · 2025Article
- The Dynamics of Long Terminal Repeat Retrotransposon Proliferation and Decay Drive the Evolution of Genome Size Variation in Capsicum.Plants (Basel, Switzerland) · 2025Article
- Article
- Allotetraploid nature of a wild potato species, Solanum stoloniferum Schlechtd. et Bché., as revealed by whole-genome sequencing.The Plant journal : for cell and molecular biology · 2025Article
- Evolution of Einkorn wheat centromeres is driven by the mutualistic interplay of two LTR retrotransposons.Mobile DNA · 2024Article
- Differences in the intraspecies copy number variation of Arabidopsis thaliana conserved and nonconserved miRNA genes.Functional & integrative genomics · 2023Article
- The nature and genomic landscape of repetitive DNA classes in Chrysanthemum nankingense shows recent genomic changes.Annals of botany · 2023Article
- Transposable Elements in the Revealing of Polymorphism-Based Differences in the Seeds of Flax Varieties Grown in Remediated Chernobyl Area.Plants (Basel, Switzerland) · 2022Article
- Review
- Finding and Characterizing Repeats in Plant Genomes.Methods in molecular biology (Clifton, N.J.) · 2022Article
- Reprogramming of RNA silencing triggered by cucumber mosaic virus infection in Arabidopsis.Genome biology · 2021Article
- The Dynamism of Transposon Methylation for Plant Development and Stress Adaptation.International journal of molecular sciences · 2021Review
- Full-length annotation with multistrategy RNA-seq uncovers transcriptional regulation of lncRNAs in cotton.Plant physiology · 2021Article
- Coconut genome assembly enables evolutionary analysis of palms and highlights signaling pathways involved in salt tolerance.Communications biology · 2021Article
- CicerSpTEdb: A web-based database for high-resolution genome-wide identification of transposable elements in Cicer species.PloS one · 2021Article
- Diversity, dynamics and effects of long terminal repeat retrotransposons in the model grass Brachypodium distachyon.The New phytologist · 2020Article
- Genome Size Evolution Mediated by Gypsy Retrotransposons in Brassicaceae.Genomics, proteomics & bioinformatics · 2020Article
- Article
28 more citing papers are in PubMed but not listed here.
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
1 author at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundGenome evolution and size variation in multicellular organisms are profoundly influenced by the activity of retrotransposons. In higher eukaryotes with compact genomes retrotransposons are found in lower copy numbers than in larger genomes, which could be due to either suppression of transposition or to elimination of insertions, and are non-randomly distributed along the chromosomes. The evolutionary mechanisms constraining retrotransposon copy number and chromosomal distribution are still poorly understood.
resultsI investigated the evolutionary dynamics of long terminal repeat (LTR)-retrotransposons in the compact Arabidopsis thaliana genome, using an automated method for obtaining genome-wide, age and physical distribution profiles for different groups of elements, and then comparing the distributions of young and old insertions. Elements of the Pseudoviridae family insert randomly along the chromosomes and have been recently active, but insertions tend to be lost from euchromatic regions where they are less likely to fix, with a half-life estimated at approximately 470,000 years. In contrast, members of the Metaviridae (particularly Athila) preferentially target heterochromatin, and were more active in the past.
conclusionDiverse evolutionary mechanisms have constrained both the copy number and chromosomal distribution of retrotransposons within a single genome. In A. thaliana, their non-random genomic distribution is due to both selection against insertions in euchromatin and preferential targeting of heterochromatin. Constant turnover of euchromatic insertions and a decline in activity for the elements that target heterochromatin have both limited the contribution of retrotransposon DNA to genome size expansion in A. thaliana.
Indexed as
Identifiers
What OpenQuestion holds
Registered trials
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.