Plant & Animal Genomes XIV Conference

January 14-18, 2006
Town & Country Convention Center
San Diego, CA

Pack-Mule Transposable Elements Mediate Gene Evolution In Plants

Ning Jiang¹ , Zhirong Bao² , Xiaoyu Zhang³ , Dawn Holligan⁴ , Sean R. Eddy⁵ , Susan R. Wessler⁴

¹  Dept. of Horticulture, Michigan State University, East Lansing, MI 48824, USA

²  Dept. of Genome Sciences, University of Washington, Seattle, WA 98195, USA

³  Dept. of Molecular, Cell, and Developmental Biology, Univerisity of California, Los Angeles, CA 90095, USA

⁴  Dept. of Plant Biology, University of Georgia, Athens, GA 30602, USA

⁵  Howard Hughes Medical Institute and Dept. of Genetics, Washington Univeristy, St. Louis, MO 63108, USA

Mutator-like transposable elements (MULEs) are found in many eukaryotic genomes and are especially prevalent in higher plants. In maize, rice and Arabidopsis a few MULEs were shown to carry fragments of cellular genes. These chimeric elements are called Pack-MULEs in this study. The abundance of MULEs in rice (a monocot plant) and the availability of most of the genome sequence permitted a systematic analysis of the prevalence and nature of Pack-MULEs in an entire genome. Here we report that there are over 3000 Pack-MULEs in rice containing fragments derived from more than 1000 cellular genes. Pack-MULEs frequently contain fragments from multiple chromosomal loci that are fused to form new ORFs, some of which are expressed as chimeric transcripts. About 5% of the Pack-MULEs are represented in cDNA collections. Functional analysis of amino acid sequences and proteomic data suggest that some captured gene fragments may be functional. Comparison of the cellular genes and Pack-MULE counterparts indicates that fragments of genomic DNA have been captured, rearranged and amplified over millions of years. In addition, an analysis of 32 Mb genomic sequences from Lotus japonicus, a dicot plant, indicates that the Pack-MULEs in L. japonicus are similar to those in rice in terms of copy number, expression level, and distribution. Given the abundance of Pack-MULEs in both rice and L. japonicus, as well as the widespread occurrence of MULEs in all characterized plant genomes, gene fragment acquisition by Pack-MULEs may represent an important new mechanism for the evolution of genes in higher plants.