ArticleThe Plant cell2011
Targeted identification of short interspersed nuclear element families shows their widespread existence and extreme heterogeneity in plant genomes.
Article in The Plant cell, 2011. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 72 papers.
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Who cites it
72 citing papers in PubMed, 134 citations in OpenAlex.
- A comprehensive map of the bovine mobilome and their epigenetic regulation of mastitis.Functional & integrative genomics · 2026Article
- Long-Standing Activity with Characteristic Genomic Insertion Signatures in Reptilian Bov-B LINEs and Associated Sauria SINEs.Biology · 2026Article
- Evolutionary Study of Transposable Elements: Structural Characterization and Phylogenomic Profiling in Plant Genomes.Journal of molecular evolution · 2026Review
- First genome assemblies of Neotropical Thoracobombus bumblebees Bombus pauloensis and Bombus pullatus.G3 (Bethesda, Md.) · 2026Article
- Massive proliferation of retrotransposons contributes to genome size expansion in species of the Pseudocercospora genus.Mobile DNA · 2026Article
- A pangenome of maize provides genetic insights into drought resistance.Nature genetics · 2025Article
- TEtrimmer: a tool to automate the manual curation of transposable elements.Nature communications · 2025Article
- Conservative evolution of genetic and genomic features inbioRxiv : the preprint server for biology · 2025Article
- DNA gains and losses in gigantic genomes do not track differences in transposable element-host silencing interactions.Communications biology · 2025Article
- Construction of a comprehensive library of repeated sequences for the annotation of Citrus genomes.BMC genomic data · 2025Article
- A multidisciplinary and integrative review of the structural genome and epigenome of Capsicum L. species.Planta · 2025Review
- Accelerating de novo SINE annotation in plant and animal genomes.Mobile DNA · 2024Article
- HiTE: a fast and accurate dynamic boundary adjustment approach for full-length transposable element detection and annotation.Nature communications · 2024Article
- Chromosome-level genome assembly of Solanum pimpinellifolium.Scientific data · 2024Article
- Plastid DNA is a major source of nuclear genome complexity and of RNA genes in the orphan crop moringa.BMC plant biology · 2024Article
- Extreme genome scrambling in marine planktonicGenome research · 2024Article
- Profiling genome-wide methylation in two maples: Fine-scale approaches to detection with nanopore technology.Evolutionary applications · 2024Article
- Review
- Repetitive DNA sequence detection and its role in the human genome.Communications biology · 2023Review
- Young SINEs in pig genomes impact gene regulation, genetic diversity, and complex traits.Communications biology · 2023Article
12 more citing papers are in PubMed but not listed here.
Corrections and comments
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Authors and funding
6 authors at 2 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Short interspersed nuclear elements (SINEs) are non-long terminal repeat retrotransposons that are highly abundant, heterogeneous, and mostly not annotated in eukaryotic genomes. We developed a tool designated SINE-Finder for the targeted discovery of tRNA-derived SINEs. We analyzed sequence data of 16 plant genomes, including 13 angiosperms and three gymnosperms and identified 17,829 full-length and truncated SINEs falling into 31 families showing the widespread occurrence of SINEs in higher plants. The investigation focused on potato (Solanum tuberosum), resulting in the detection of seven different SolS SINE families consisting of 1489 full-length and 870 5' truncated copies. Consensus sequences of full-length members range in size from 106 to 244 bp depending on the SINE family. SolS SINEs populated related species and evolved separately, which led to some distinct subfamilies. Solanaceae SINEs are dispersed along chromosomes and distributed without clustering but with preferred integration into short A-rich motifs. They emerged more than 23 million years ago and were species specifically amplified during the radiation of potato, tomato (Solanum lycopersicum), and tobacco (Nicotiana tabacum). We show that tobacco TS retrotransposons are composite SINEs consisting of the 3' end of a long interspersed nuclear element integrated downstream of a nonhomologous SINE family followed by successfully colonization of the genome. We propose an evolutionary scenario for the formation of TS as a spontaneous event, which could be typical for the emergence of SINE families.
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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.