A novel method for identifying polymorphic transposable elements via scanning of high-throughput short reads.
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.
State Key Laboratory for Biology of Plant Diseases and Insect Pest, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, China kanghouxiangcaas@163.com wang.620@osu.edu.
Houxiang
H
Kang
State Key Laboratory for Biology of Plant Diseases and Insect Pest, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, China Department of Agronomy, Hunan Agricultural University, Changsha, Hunan 410128, China.
Dan
D
Zhu
Department of Plant Pathology, Institute of Vegetables and flowers, Chinese Academy of Agriculture Science, Beijing 100081, China.
Runmao
R
Lin
Molecular and Cellular Imaging Center - Columbus, Ohio Agricultural Research and Development Center, Columbus, OH 43210, USA.
Stephen Obol
SO
Opiyo
Department of Horticulture, Michigan State University, 1066 Bogue Street, East Lansing, MI 48823, USA.
Ning
N
Jiang
Department of Plant Biology, Michigan State University, East Lansing, MI 48823, USA.
Shin-Han
SH
Shiu
State Key Laboratory for Biology of Plant Diseases and Insect Pest, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, China Department of Plant Pathology, Ohio State University, Columbus, OH 43210, USA kanghouxiangcaas@163.com wang.620@osu.edu.
Guo-Liang
GL
Wang
D000465:Algorithms; D004251:DNA Transposable Elements; D004271:DNA, Fungal / Q000737:chemistry / Q000235:genetics; D016681:Genome, Fungal; D059014:High-Throughput Nucleotide Sequencing / Q000379:methods*; D020082:Magnaporthe / Q000235:genetics*; D011110:Polymorphism, Genetic; D017422:Sequence Analysis, DNA / Q000379:methods*
D004251:DNA Transposable Elements; D004271:DNA, Fungal
high-throughput sequencing; maize; polymorphic transposon; rice blast fungus