ArticleGenetics2009
A new family of Ty1-copia-like retrotransposons originated in the tomato genome by a recent horizontal transfer event.
Article in Genetics, 2009. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 30 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
30 citing papers in PubMed, 64 citations in OpenAlex.
- Wild tomato genome assemblies reveal structural variants and repeat content act as recombination barriers.Nature communications · 2026Article
- Evolutionary Study of Transposable Elements: Structural Characterization and Phylogenomic Profiling in Plant Genomes.Journal of molecular evolution · 2026Review
- Uncovering the genome evolutionary dynamics of the Mediterranean endemic palm Chamaerops humilis.BMC plant biology · 2026Article
- A de novo Gene Promotes Seed Germination Under Drought Stress in Arabidopsis.Molecular biology and evolution · 2025Article
- Perturbations in the Carotenoid Biosynthesis Pathway in Tomato Fruit Reactivate the Leaf-Specific Phytoene Synthase 2.Frontiers in plant science · 2022Article
- Horizontal Gene Transfers in Plants.Life (Basel, Switzerland) · 2021Review
- A Predictive Approach to Infer the Activity and Natural Variation of Retrotransposon Families in Plants.Methods in molecular biology (Clifton, N.J.) · 2021Article
- Transcription of lncRNARNA biology · 2020Article
- Comparative study of3 Biotech · 2020Article
- Environmental and epigenetic regulation of Rider retrotransposons in tomato.PLoS genetics · 2019Article
- FIT-Binding Proteins and Their Functions in the Regulation of Fe Homeostasis.Frontiers in plant science · 2019Review
- Horizontal acquisition of transposable elements and viral sequences: patterns and consequences.Current opinion in genetics & development · 2018Review
- Genetic exchange in eukaryotes through horizontal transfer: connected by the mobilome.Mobile DNA · 2018Review
- Diversity, distribution and dynamics of full-length Copia and Gypsy LTR retroelements in Solanum lycopersicum.Genetica · 2017Article
- Mapping and Characterization of theFrontiers in plant science · 2017Article
- Article
- Isolation, characterization, and marker utility of KCRE1, a transcriptionally active Ty1/copia retrotransposon from Kandelia candel.Molecular genetics and genomics : MGG · 2016Article
- Large distribution and high sequence identity of a Copia-type retrotransposon in angiosperm families.Plant molecular biology · 2015Article
- Article
- Genomic localization of AtRE1 and AtRE2, copia-type retrotransposons, in natural variants of Arabidopsis thaliana.Molecular genetics and genomics : MGG · 2014Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
5 authors at 3 institutions in 2 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Rider is a novel and recently active Ty1-copia-like retrotransposon isolated from the T3238fer mutant of tomato. Structurally, it is delimited by a duplication of target sites and contains two long terminal direct repeats and an internal open reading frame, which encodes a Ty1-copia-type polyprotein with characteristic protein domains required for retrotransposition. The family of Rider elements has an intermediate copy number and is scattered in the chromosomes of tomato. Rider family members in the tomato genome share high sequence similarity, but different structural groups were identified (full-size elements, deletion derivatives, and solo LTRs). Southern blot analysis in Solanaceae species showed that Rider was a Lycopersicon-specific element. Sequence analysis revealed that among other plants, two Arabidopsis elements (named as Rider-like 1 and Rider-like 2) are most similar to Rider in both the coding and noncoding regions. RT-PCR analysis indicates that Rider is constitutively expressed in tomato plants. The phylogeny-based parsimony analysis and the sequence substitution analyses of these data suggest that these Rider-like elements originated from a recent introgression of Rider into the tomato genome by horizontal transfer 1-6 million years ago. Considering its transcriptional activity and the recent insertion of the element into at least two genes, Rider is a recently active retrotransposon in the tomato genome.
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.