ArticleBMC genomics2010
SoyTEdb: a comprehensive database of transposable elements in the soybean genome.
Article in BMC genomics, 2010. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 80 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
80 citing papers in PubMed, 147 citations in OpenAlex.
- Comparative evaluation of GWAS-prioritized SNP, SSR, and insertion-type structural variant marker panels for genomic prediction in soybean.TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik · 2026Article
- Characterization of disomic alien addition lines from an intersubgeneric cross between Glycine max and G. tomentella and phenotypic variation within those lines and their progenies.Plant molecular biology · 2026Article
- Evolutionary Study of Transposable Elements: Structural Characterization and Phylogenomic Profiling in Plant Genomes.Journal of molecular evolution · 2026Review
- EDTA-GUI: a plant-optimized graphical implementation of the EDTA pipeline enabling lineage-level classification and analysis.BMC genomics · 2026Article
- CREATE: a novel attention-based framework for efficient classification of transposable elements.Briefings in bioinformatics · 2025Article
- Updated resource of 180K soybean SNP genotyping array based on the T2T reference genome.PloS one · 2025Article
- Decoding the complete organelle genomic architecture of Stewartia gemmata: an early-diverging species in Theaceae.BMC genomics · 2024Article
- Pan-centromere reveals widespread centromere repositioning of soybean genomes.Proceedings of the National Academy of Sciences of the United States of America · 2023Article
- Recombination hotspots in soybean [Glycine max (L.) Merr.].G3 (Bethesda, Md.) · 2023Article
- Abundance of Transgene Transcript Variants Associated with Somatically Active TransgenicInternational journal of molecular sciences · 2023Article
- A retrotransposon insertion in theProceedings of the National Academy of Sciences of the United States of America · 2023Article
- Genome-Wide Comparison of Structural Variations and Transposon Alterations in Soybean Cultivars Induced by Spaceflight.International journal of molecular sciences · 2022Article
- TransposonUltimate: software for transposon classification, annotation and detection.Nucleic acids research · 2022Article
- POWR1 is a domestication gene pleiotropically regulating seed quality and yield in soybean.Nature communications · 2022Article
- Genetic and Genomic Resources for Soybean Breeding Research.Plants (Basel, Switzerland) · 2022Review
- Heterosis and Differential DNA Methylation in Soybean Hybrids and Their Parental Lines.Plants (Basel, Switzerland) · 2022Article
- Combined use of Oxford Nanopore and Illumina sequencing yields insights into soybean structural variation biology.BMC biology · 2022Article
- Progress in soybean functional genomics over the past decade.Plant biotechnology journal · 2022Review
- Finding and Characterizing Repeats in Plant Genomes.Methods in molecular biology (Clifton, N.J.) · 2022Article
- K-mer counting and curated libraries drive efficient annotation of repeats in plant genomes.The plant genome · 2021Article
20 more citing papers are in PubMed but not listed here.
Corrections and comments
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Authors and funding
7 authors at 3 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundTransposable elements are the most abundant components of all characterized genomes of higher eukaryotes. It has been documented that these elements not only contribute to the shaping and reshaping of their host genomes, but also play significant roles in regulating gene expression, altering gene function, and creating new genes. Thus, complete identification of transposable elements in sequenced genomes and construction of comprehensive transposable element databases are essential for accurate annotation of genes and other genomic components, for investigation of potential functional interaction between transposable elements and genes, and for study of genome evolution. The recent availability of the soybean genome sequence has provided an unprecedented opportunity for discovery, and structural and functional characterization of transposable elements in this economically important legume crop. DESCRIPTION: Using a combination of structure-based and homology-based approaches, a total of 32,552 retrotransposons (Class I) and 6,029 DNA transposons (Class II) with clear boundaries and insertion sites were structurally annotated and clearly categorized, and a soybean transposable element database, SoyTEdb, was established. These transposable elements have been anchored in and integrated with the soybean physical map and genetic map, and are browsable and visualizable at any scale along the 20 soybean chromosomes, along with predicted genes and other sequence annotations. BLAST search and other infrastracture tools were implemented to facilitate annotation of transposable elements or fragments from soybean and other related legume species. The majority (> 95%) of these elements (particularly a few hundred low-copy-number families) are first described in this study.
conclusionSoyTEdb provides resources and information related to transposable elements in the soybean genome, representing the most comprehensive and the largest manually curated transposable element database for any individual plant genome completely sequenced to date. Transposable elements previously identified in legumes, the third largest family of flowering plants, are relatively scarce. Thus this database will facilitate structural, evolutionary, functional, and epigenetic analyses of transposable elements in soybean and other legume species.
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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.