ArticleGenetica2017
Diversity, distribution and dynamics of full-length Copia and Gypsy LTR retroelements in Solanum lycopersicum.
Article in Genetica, 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 18 papers.
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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.
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Who cites it
18 citing papers in PubMed, 36 citations in OpenAlex.
- LTR retrotransposons shape genome architecture, function, and evolution in diverse plant species.Frontiers in plant science · 2026Article
- Lineage-specific amplification and epigenetic regulation of LTR-retrotransposons contribute to the structure, evolution, and function of Fabaceae species.BMC genomics · 2023Article
- A large-scale assessment of the quality of plant genome assemblies using the LTR assembly index.AoB PLANTS · 2023Article
- Impact of LTR-Retrotransposons on Genome Structure, Evolution, and Function in Curcurbitaceae Species.International journal of molecular sciences · 2022Article
- Automatic curation of LTR retrotransposon libraries from plant genomes through machine learning.Journal of integrative bioinformatics · 2022Article
- Hybridization and polyploidization effects on LTR-retrotransposon activation in potato genome.Journal of plant research · 2022Article
- Full-length LTR retroelements in Capsicum annuum revealed a few species-specific family bursts with insertional preferences.Chromosome research : an international journal on the molecular, supramolecular and evolutionary aspects of chromosome biology · 2021Article
- Transcriptional activity of transposable elements along an elevational gradient in Arabidopsis arenosa.Mobile DNA · 2021Article
- Article
- Genomic re-assessment of the transposable element landscape of the potato genome.Plant cell reports · 2020Article
- Genome relationships and LTR-retrotransposon diversity in three cultivated Capsicum L. (Solanaceae) species.BMC genomics · 2020Article
- Article
- Functional characterization of a strong promoter of the early light-inducible protein gene from tomato.Planta · 2019Article
- Retrotransposons in Plant Genomes: Structure, Identification, and Classification through Bioinformatics and Machine Learning.International journal of molecular sciences · 2019Review
- Low coverage sequencing for repetitive DNA analysis in Passiflora edulis Sims: citogenomic characterization of transposable elements and satellite DNA.BMC genomics · 2019Article
- The landscape of transposable elements and satellite DNAs in the genome of a dioecious plant spinach (Mobile DNA · 2019Article
- Analysis of retrotransposon abundance, diversity and distribution in holocentric Eleocharis (Cyperaceae) genomes.Annals of botany · 2018Article
- An InDel in the Promoter ofThe Plant cell · 2017Article
Corrections and comments
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Authors and funding
5 authors at 3 institutions in 1 country.
Funding
Abstract
Transposable elements are the most abundant components of plant genomes and can dramatically induce genetic changes and impact genome evolution. In the recently sequenced genome of tomato (Solanum lycopersicum), the estimated fraction of elements corresponding to retrotransposons is nearly 62%. Given that tomato is one of the most important vegetable crop cultivated and consumed worldwide, understanding retrotransposon dynamics can provide insight into its evolution and domestication processes. In this study, we performed a genome-wide in silico search of full-length LTR retroelements in the tomato nuclear genome and annotated 736 full-length Gypsy and Copia retroelements. The dispersion level across the 12 chromosomes, the diversity and tissue-specific expression of those elements were estimated. Phylogenetic analysis based on the retrotranscriptase region revealed the presence of 12 major lineages of LTR retroelements in the tomato genome. We identified 97 families, of which 77 and 20 belong to the superfamilies Copia and Gypsy, respectively. Each retroelement family was characterized according to their element size, relative frequencies and insertion time. These analyses represent a valuable resource for comparative genomics within the Solanaceae, transposon-tagging and for the design of cultivar-specific molecular markers in tomato.
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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.