title: An active DNA transposon family in rice.
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.
authors.affiliation: Department of Plant Biology, University of Georgia, Athens, Georgia 30602, USA.
authors.forename: Ning
authors.initials: N
authors.lastname: Jiang
authors.forename: Zhirong
authors.initials: Z
authors.lastname: Bao
authors.forename: Xiaoyu
authors.initials: X
authors.lastname: Zhang
authors.forename: Hirohiko
authors.initials: H
authors.lastname: Hirochika
authors.forename: Sean R
authors.initials: SR
authors.lastname: Eddy
authors.forename: Susan R
authors.initials: SR
authors.lastname: McCouch
authors.forename: Susan R
authors.initials: SR
authors.lastname: Wessler
mesh_terms: D000595:Amino Acid Sequence; D001483:Base Sequence; D002460:Cell Line; D019295:Computational Biology; D004251:DNA Transposable Elements / Q000235:genetics*; D030561:Databases, Nucleic Acid; D004777:Environment; D018628:Gene Dosage; D018745:Genome, Plant; D008969:Molecular Sequence Data; D016254:Mutagenesis, Insertional / Q000235:genetics*; D016366:Open Reading Frames / Q000235:genetics; D012275:Oryza / Q000145:classification / Q000235:genetics*; D011995:Recombination, Genetic / Q000235:genetics; D012091:Repetitive Sequences, Nucleic Acid / Q000235:genetics
chemical_list: D004251:DNA Transposable Elements