ArticleDNA research : an international journal for rapid publication of reports on genes and genomes2016
A novel method for identifying polymorphic transposable elements via scanning of high-throughput short reads.
Article in DNA research : an international journal for rapid publication of reports on genes and genomes, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 11 papers.
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Who cites it
11 citing papers in PubMed.
- A transposon insertion in the 5' UTR of OsPT1 reprograms its expression pattern and promotes cadmium accumulation in rice grains.Plant communications · 2026Article
- The Dynamics of Long Terminal Repeat Retrotransposon Proliferation and Decay Drive the Evolution of Genome Size Variation in Capsicum.Plants (Basel, Switzerland) · 2025Article
- RETRACTED: Genotyping strategies for tissues fixed with various embalming fluids for human identification, databasing, and traceability.Journal of forensic sciences · 2025Article
- Identification of two novel rice S genes through combination of association and transcription analyses with gene-editing technology.Plant biotechnology journal · 2023Article
- Chromosome-scale genome assembly of a Japanese chili pepper landrace, Capsicum annuum 'Takanotsume'.DNA research : an international journal for rapid publication of reports on genes and genomes · 2023Article
- Transposable Elements Contribute to Genome Dynamics and Gene Expression Variation in the Fungal Plant Pathogen Verticillium dahliae.Genome biology and evolution · 2021Article
- Miniature inverted-repeat transposable elements (MITEs), derived insertional polymorphism as a tool of marker systems for molecular plant breeding.Molecular biology reports · 2020Review
- Generic Repeat Finder: A High-Sensitivity Tool for Genome-Wide De Novo Repeat Detection.Plant physiology · 2019Article
- Identification of an active miniature inverted-repeat transposable element mJing in rice.The Plant journal : for cell and molecular biology · 2019Article
- Article
- Development of AhMITE1 markers through genome-wide analysis in peanut (Arachis hypogaea L.).BMC research notes · 2018Article
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Authors and funding
7 authors.
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Abstract
Identification of polymorphic transposable elements (TEs) is important because TE polymorphism creates genetic diversity and influences the function of genes in the host genome. However, de novo scanning of polymorphic TEs remains a challenge. Here, we report a novel computational method, called PTEMD (polymorphic TEs and their movement detection), for de novo discovery of genome-wide polymorphic TEs. PTEMD searches highly identical sequences using reads supported breakpoint evidences. Using PTEMD, we identified 14 polymorphic TE families (905 sequences) in rice blast fungus Magnaporthe oryzae, and 68 (10,618 sequences) in maize. We validated one polymorphic TE family experimentally, MoTE-1; all MoTE-1 family members are located in different genomic loci in the three tested isolates. We found that 57.1% (8 of 14) of the PTEMD-detected polymorphic TE families in M. oryzae are active. Furthermore, our data indicate that there are more polymorphic DNA transposons in maize than their counterparts of retrotransposons despite the fact that retrotransposons occupy largest fraction of genomic mass. We demonstrated that PTEMD is an effective tool for identifying polymorphic TEs in M. oryzae and maize genomes. PTEMD and the genome-wide polymorphic TEs in M. oryzae and maize are publically available at http://www.kanglab.cn/blast/PTEMD_V1.02.htm.
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