Introduction

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.

Publications

  1. A novel method for identifying polymorphic transposable elements via scanning of high-throughput short reads.
    Cite this
    Kang H, Zhu D, Lin R, Opiyo SO, Jiang N, Shiu SH, Wang GL, 2016-06-01 - DNA research : an international journal for rapid publication of reports on genes and genomes

Credits

  1. Houxiang Kang
    Developer

    State Key Laboratory for Biology of Plant Diseases and Insect Pest, Institute of Plant Protection, China

  2. Dan Zhu
    Developer

    State Key Laboratory for Biology of Plant Diseases and Insect Pest, Institute of Plant Protection, China

  3. Runmao Lin
    Developer

    Department of Plant Pathology, Institute of Vegetables and flowers, China

  4. Stephen Obol Opiyo
    Developer

    Molecular and Cellular Imaging Center - Columbus, Ohio Agricultural Research and Development Center, United States of America

  5. Ning Jiang
    Developer

    Department of Horticulture, Michigan State University, United States of America

  6. Shin-Han Shiu
    Developer

    Department of Plant Biology, Michigan State University, United States of America

  7. Guo-Liang Wang
    Investigator

    State Key Laboratory for Biology of Plant Diseases and Insect Pest, Institute of Plant Protection, China

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Summary
AccessionBT001444
Tool TypeApplication
Category
PlatformsLinux/Unix
TechnologiesPerl
User InterfaceTerminal Command Line
Download Count0
Country/RegionChina
Submitted ByGuo-Liang Wang