FARE, a New Family of Foldback Transposons in Arabidopsis

• Published in: Genetics (Austin) Vol. 156; no. 4; pp. 1983 - 1995
• Main Authors: Windsor, Aaron J, Waddell, Candace S
• Format: Journal Article
• Language: English
• Published: United States Genetics Soc America 01.12.2000; Genetics Society of America
• Subjects: Amino Acid Sequence; Arabidopsis - genetics; Arabidopsis thaliana; Base Pairing; Base Sequence; Consensus Sequence; Deoxyribonucleic acid; DNA; DNA Transposable Elements - genetics; DNA, Plant - genetics; DNA, Plant - ultrastructure; Gene Duplication; Genetics; Molecular Sequence Data; Multigene Family; Nucleic Acid Conformation; Phylogeny; Plant Proteins - genetics; Polymerase Chain Reaction; Protein Structure, Tertiary; Sequence Alignment; Sequence Homology, Amino Acid; transposon FARE
• ISSN: 0016-6731; 1943-2631; 1943-2631
• DOI: 10.1093/genetics/156.4.1983

A new family of transposons, FARE, has been identified in Arabidopsis. The structure of these elements is typical of foldback transposons, a distinct subset of mobile DNA elements found in both plants and animals. The ends of FARE elements are long, conserved inverted repeat sequences typically 550 bp in length. These inverted repeats are modular in organization and are predicted to confer extensive secondary structure to the elements. FARE elements are present in high copy number, are heterogeneous in size, and can be divided into two subgroups. FARE1's average 1.1 kb in length and are composed entirely of the long inverted repeats. FARE2's are larger, up to 16.7 kb in length, and contain a large internal region in addition to the inverted repeat ends. The internal region is predicted to encode three proteins, one of which bears homology to a known transposase. FARE1.1 was isolated as an insertion polymorphism between the ecotypes Columbia and Nossen. This, coupled with the presence of 9-bp target-site duplications, strongly suggests that FARE elements have transposed recently. The termini of FARE elements and other foldback transposons are imperfect palindromic sequences, a unique organization that further distinguishes these elements from other mobile DNAs.