A Highly Conserved, Small LTR Retrotransposon that Preferentially Targets Genes in Grass Genomes

Small LTR Retrotransposon that Preferentially Targets Genes in Grass Genomes. PLoS ONE 7(2): e32010. doi:10.1371/journal.pone.0032010 A Highly Conserved, Small LTR Retrotransposon that Preferentially Targets Genes in Grass Genomes Dongying Gao 0 Jinfeng Chen 0 Mingsheng Chen 0 Blake C. Meyers 0 Scott Jackson 0 Mark A. Batzer, Louisiana State University, United States of America 0 1 Center for Applied Genetic Technologies and Institute for Plant Breeding Genetics and Genomics, University of Georgia , Athens , Georgia , United States of America, 2 State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences , Beijing , China , 3 Department of Plant and Soil Sciences, and Delaware Biotechnology Institute, University of Delaware , Newark, Delaware , United States of America LTR retrotransposons are often the most abundant components of plant genomes and can impact gene and genome evolution. Most reported LTR retrotransposons are large elements (.4 kb) and are most often found in heterochromatic (gene poor) regions. We report the smallest LTR retrotransposon found to date, only 292 bp. The element is found in rice, maize, sorghum and other grass genomes, which indicates that it was present in the ancestor of grass species, at least 5080 MYA. Estimated insertion times, comparisons between sequenced rice lines, and mRNA data indicate that this element may still be active in some genomes. Unlike other LTR retrotransposons, the small LTR retrotransposons (SMARTs) are distributed throughout the genomes and are often located within or near genes with insertion patterns similar to MITEs (miniature inverted repeat transposable elements). Our data suggests that insertions of SMARTs into or near genes can, in a few instances, alter both gene structures and gene expression. Further evidence for a role in regulating gene expression, SMART-specific small RNAs (sRNAs) were identified that may be involved in gene regulation. Thus, SMARTs may have played an important role in genome evolution and genic innovation and may provide a valuable tool for gene tagging systems in grass. - Transposable elements (TEs) are mobile DNA sequences found in most eukaryote genomes. Once considered junk DNA, transposons are now known to impact both gene and genome evolution [13]. In addition to their use for insertional mutagenesis, TEs are involved in many chromosome rearrangements, gene regulation and provide raw material for genetic innovation [46]. Furthermore, transposons also serve as essential components of heterochromatin maintaining centromeric and telomeric stability and heterochromatic silencing [79]. Transposons are divided into two major classes: Class II transposons that move to new locations via a cut and paste model or by a rolling-circle mechanism; and Class I transposons or retrotransposons that mobilize through a copy and paste model by which retrotransposon copies are integrated into new positions in the genome [10]. Long terminal repeat (LTR) retrotransposons are the most abundant mobile elements in the plant kingdom. In some plants, LTR retrotransposons can make up more than 70% of the genome [11]. The most typical features of LTR retrotransposons are direct LTRs that surround the internal domains (functional retrotransposases and/or other sequences) and are flanked by 4 6 bp target site duplications (TSDs). LTR retrotransposons are further subdivided into Ty1-copia (Pseudoviridae) and Ty3-gypsy (Metaviridae) superfamilies according to sequence divergence and the order of encoded gene products. Two other nonautonomous LTR-retrotransposons have been identified in plants, terminalrepeat retrotransposons in miniature (TRIM) and large retrotransposon derivatives (LARD) [1215]. These two retrotransposons share similar sequence structures with Ty1-copia and Ty3gypsy LTR retrotransposons but do not encode functional retrotransposases and their mobility is most likely catalyzed by other retrotransposons [16]. In contrast to LTR retroelements in other organisms, LTR retrotransposons in plants are often present in very high copy numbers. For instance, a single Ty1-copia retrotransposon family, BARE1, exists in the barley genome in more than 26105 copies and comprises about 9.6% of the genome [17]. Moreover, different LTR retrotransposons in plants can show distinct chromosomal distribution patterns. Some LTR retrotransposons are found in intergenic regions1 but most appear to be concentrated in highly heterochromatic regions (centromeres, pericentromeres, telomeres) [16,1823]. Furthermore, plant LTR retrotransposons are often large ranging from 410 kb, on average, and can even be as large as 1822 kb and have LTRs that are over 5 kb [1,24,25]. Due to their replicative transposition and large sizes, the amplification of LTR retrotransposons can rapidly increase plant genome sizes over a relatively short time and is considered one of the primary contributors to the C-value paradox in plants [26]. For example, the genome size of a diploid wild rice, O. australiensis, is more than twice the diploid cultivated species and this is due to recent bursts of 3 LTR retrotransposon families which contribute more than 60% of the O. australiensis genome [27]. Active LTR retrotransposons not only can increase the host genome size but they can also result in deleterious mutations [1 3]. Thus, several strategies have evolved to prevent uncontrolled amplifications of LTR retrotransposons. First is the transcriptional silencing mechanism mediated through DNA methylation and chromatin modification to suppress transcriptional activity of transposons. Secondly, small RNA (sRNA) molecules can be incorporated into the RNA-induced silencing complex (RISC) and target LTR retrotransposons transcripts for post-transcriptional silencing [28,29]. In addition, to counteract genome obesity, deletion of retrotransposons may occur through unequal homologous or illegitimate recombination between LTRs [21,30,31]. We discovered an unusually small, novel LTR retrotransposon named FRetro129 in O. brachyantha, a wild rice species, that is 292 bp with 85-bp direct terminal repeats. This is the smallest LTR retrotransposon reported thus far. Elements homologous to FRetro129 were found in other grass family genomes but not outside the grass family. Despite an ancient and/or possible multiple origins, FRetro129 and its homologues may yet be active in some genomes. Unlike most LTR retrotransposons in plants that are found in heterochromatic regions, this small retroelement is enriched within or near genes, a similar pattern to the DNA transposon, miniature inverted repeat transposable elements (MITEs). Our data indicates that the small retrotransposons may be involved in genic innovation and gene regulation. This small element family advances our knowledge about retrotransposons their role in gene/genome evolution and may provide a tool for functional gene studies in the gras (...truncated)