ArticleF1000Research2021
An Atlas of Plant Transposable Elements.
Article in F1000Research, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 15 papers.
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Who cites it
15 citing papers in PubMed.
- MaizeGDB Phylostrata Tool: exploring evolutionary origins of maize proteins.Bioinformatics advances · 2026Article
- Comparative Analysis of Transposable Element Evolution in Crustaceans.Genome biology and evolution · 2025Article
- Patterns and mechanisms of fungal genome plasticity.Current biology : CB · 2025Review
- Deciphering recent transposition patterns in plants through comparison of 811 genome assemblies.Plant biotechnology journal · 2025Article
- Comprehensive study of tRNA-derived fragments in plants for biotic stress responses.Functional & integrative genomics · 2025Article
- Epigenetic factors direct synergistic and antagonistic regulation of transposable elements in Arabidopsis.Plant physiology · 2024Article
- CAM evolution is associated with gene family expansion in an explosive bromeliad radiation.The Plant cell · 2024Article
- Causes and Consequences of Varying Transposable Element Activity: An Evolutionary Perspective.Annual review of genomics and human genetics · 2024Review
- Genomic decoding of Theobroma grandiflorum (cupuassu) at chromosomal scale: evolutionary insights for horticultural innovation.GigaScience · 2024Article
- Deciphering shared attributes of plant long non-coding RNAs through a comparative computational approach.Scientific reports · 2023Article
- From qualitative to quantitative: the state of the art and challenges for plant synthetic biology.Quantitative biology (Beijing, China) · 2023Review
- Taming transposable elements in livestock and poultry: a review of their roles and applications.Genetics, selection, evolution : GSE · 2023Review
- PlantLTRdb: An interactive database for 195 plant species LTR-retrotransposons.Frontiers in plant science · 2023Article
- The first long-read nuclear genome assembly of Oryza australiensis, a wild rice from northern Australia.Scientific reports · 2022Article
- An Atlas of Plant Transposable Elements.F1000Research · 2021Article
Corrections and comments
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Authors and funding
6 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Advances in genomic sequencing have recently offered vast opportunities for biological exploration, unraveling the evolution and improving our understanding of Earth biodiversity. Due to distinct plant species characteristics in terms of genome size, ploidy and heterozygosity, transposable elements (TEs) are common characteristics of many genomes. TEs are ubiquitous and dispersed repetitive DNA sequences that frequently impact the evolution and composition of the genome, mainly due to their redundancy and rearrangements. For this study, we provided an atlas of TE data by employing an easy-to-use portal ( APTE website ). To our knowledge, this is the most extensive and standardized analysis of TEs in plant genomes. We evaluated 67 plant genomes assembled at chromosome scale, recovering a total of 49,802,023 TE records, representing a total of 47,992,091,043 (~47,62%) base pairs (bp) of the total genomic space. We observed that new types of TEs were identified and annotated compared to other data repositories. By establishing a standardized catalog of TE annotation on 67 genomes, new hypotheses, exploration of TE data and their influences on the genomes may allow a better understanding of their function and processes. All original code and an example of how we developed the TE annotation strategy is available on GitHub (
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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 Socratic graph.