An active DNA transposon family in rice

Nature. 2003 Jan 9;421(6919):163-7. doi: 10.1038/nature01214.

Abstract

The publication of draft sequences for the two subspecies of Oryza sativa (rice), japonica (cv. Nipponbare) and indica (cv. 93-11), provides a unique opportunity to study the dynamics of transposable elements in this important crop plant. Here we report the use of these sequences in a computational approach to identify the first active DNA transposons from rice and the first active miniature inverted-repeat transposable element (MITE) from any organism. A sequence classified as a Tourist-like MITE of 430 base pairs, called miniature Ping (mPing), was present in about 70 copies in Nipponbare and in about 14 copies in 93-11. These mPing elements, which are all nearly identical, transpose actively in an indica cell-culture line. Database searches identified a family of related transposase-encoding elements (called Pong), which also transpose actively in the same cells. Virtually all new insertions of mPing and Pong elements were into low-copy regions of the rice genome. Since the domestication of rice mPing MITEs have been amplified preferentially in cultivars adapted to environmental extremes-a situation that is reminiscent of the genomic shock theory for transposon activation.

Publication types

  • Research Support, U.S. Gov't, Non-P.H.S.

MeSH terms

  • Amino Acid Sequence
  • Base Sequence
  • Cell Line
  • Computational Biology
  • DNA Transposable Elements / genetics*
  • Databases, Nucleic Acid
  • Environment
  • Gene Dosage
  • Genome, Plant
  • Molecular Sequence Data
  • Mutagenesis, Insertional / genetics*
  • Open Reading Frames / genetics
  • Oryza / classification
  • Oryza / genetics*
  • Recombination, Genetic / genetics
  • Repetitive Sequences, Nucleic Acid / genetics

Substances

  • DNA Transposable Elements

Associated data

  • GENBANK/BK000586
  • GENBANK/BK000587
  • GENBANK/BK000588