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 polymorphic TEs remains a challenge. Recently, researchers at State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection (IPP), CAAS, have published a research paper to report a novel computer method PTEMD (polymorphic TEs and their movement detection) for de novo identifying polymorphic TEs via scanning of high-throughput short reads.

The core algorithm of PTEMD

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, indicated it may played very important function in M. oryzae mutation. 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 software and the genome-wide polymorphic TEs in M. oryzae and maize are publically available at http://www.kanglab.cn/blast/PTEMD_V1.02.htm.

Details of this paper link:
http://dnaresearch.oxfordjournals.org/content/early/2016/04/19/dnares.dsw011.abstract

Houxiang Kang
kanghouxiangcaas@163.com