ArticleThe Plant cell2012
Genome-wide characterization of nonreference transposons reveals evolutionary propensities of transposons in soybean.
Article in The Plant cell, 2012. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 28 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
28 citing papers in PubMed, 55 citations in OpenAlex.
- LTR retrotransposons shape genome architecture, function, and evolution in diverse plant species.Frontiers in plant science · 2026Article
- The Heterogeneity in the Landscape of Gene Dominance in Maize is Accompanied by Unique Chromatin Environments.Molecular biology and evolution · 2022Article
- Mutation Load in Sunflower Inversions Is Negatively Correlated with Inversion Heterozygosity.Molecular biology and evolution · 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
- Retrotransposons: How the continuous evolutionary front shapes plant genomes for response to heat stress.Frontiers in plant science · 2022Review
- Identifying new variation at the J locus, previously identified as e6, in long juvenile 'Paranagoiana' soybean.TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik · 2021Article
- Natural variation and evolutionary dynamics of transposable elements inHorticulture research · 2020Article
- ThePlant direct · 2019Article
- A reference-grade wild soybean genome.Nature communications · 2019Article
- Genomic introgression through interspecific hybridization counteracts genetic bottleneck during soybean domestication.Genome biology · 2019Article
- The Landscape ofFrontiers in plant science · 2019Article
- Chromosomal distribution of soybean retrotransposon SORE-1 suggests its recent preferential insertion into euchromatic regions.Chromosome research : an international journal on the molecular, supramolecular and evolutionary aspects of chromosome biology · 2018Article
- Recent Activity in Expanding Populations and Purifying Selection Have Shaped Transposable Element Landscapes across Natural Accessions of the Mediterranean Grass Brachypodium distachyon.Genome biology and evolution · 2018Article
- Coevolution between transposable elements and recombination.Philosophical transactions of the Royal Society of London. Series B, Biological sciences · 2017Review
- Patterns and Consequences of Subgenome Differentiation Provide Insights into the Nature of Paleopolyploidy in Plants.The Plant cell · 2017Article
- Genome-wide characterization of non-reference transposable element insertion polymorphisms reveals genetic diversity in tropical and temperate maize.BMC genomics · 2017Article
- Genome-wide characterization of non-reference transposons in crops suggests non-random insertion.BMC genomics · 2016Article
- Genome-wide Annotation and Comparative Analysis of Long Terminal Repeat Retrotransposons between Pear Species of P. bretschneideri and P. Communis.Scientific reports · 2015Article
- Genetic basis and detection of unintended effects in genetically modified crop plants.Transgenic research · 2015Review
Corrections and comments
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Authors and funding
11 authors at 6 institutions in 2 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Preferential accumulation of transposable elements (TEs), particularly long terminal repeat retrotransposons (LTR-RTs), in recombination-suppressed pericentromeric regions seems to be a general pattern of TE distribution in flowering plants. However, whether such a pattern was formed primarily by preferential TE insertions into pericentromeric regions or by selection against TE insertions into euchromatin remains obscure. We recently investigated TE insertions in 31 resequenced wild and cultivated soybean (Glycine max) genomes and detected 34,154 unique nonreference TE insertions mappable to the reference genome. Our data revealed consistent distribution patterns of the nonreference LTR-RT insertions and those present in the reference genome, whereas the distribution patterns of the nonreference DNA TE insertions and the accumulated ones were significantly different. The densities of the nonreference LTR-RT insertions were found to negatively correlate with the rates of local genetic recombination, but no significant correlation between the densities of nonreference DNA TE insertions and the rates of local genetic recombination was detected. These observations suggest that distinct insertional preferences were primary factors that resulted in different levels of effectiveness of purifying selection, perhaps as an effect of local genomic features, such as recombination rates and gene densities that reshaped the distribution patterns of LTR-RTs and DNA TEs in soybean.
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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.