The Contribution of Transposable Elements to Expressed Coding Sequence in Arabidopsis thaliana

Abstract

The goal of this study was to assess the extent to which transposable elements (TEs) have contributed to protein-coding regions in Arabidopsis thaliana. To do this, we first characterized the extent of chimeric TE-gene constructs. We compared a genome-wide TE database to genomic sequences, annotated coding regions, and EST data. The comparison revealed that 7.8% of expressed genes contained a region with close similarity to a known TE sequence. Some groups of TEs, such as helitrons, were underrepresented in exons relative to their genome-wide distribution; in contrast, Copia-like and En/Spm-like sequences were overrepresented in exons. These 7.8% percent of genes were enriched for some GO-based functions, particularly kinase activity, and lacking in other functions, notably structural molecule activity. We also examined gene family evolution for these genes. Gene family information helped clarify whether the sequence similarity between TE and gene was due to a TE contributing to the gene or, instead, the TE co-opting a portion of the gene. Most (66%) of these genes were not easily assigned to a gene family, and for these we could not infer the direction of the relationship between TE and gene. For the remainder, where appropriate, we built phylogenetic trees to infer the direction of the TE-gene relationship by parsimony. By this method, we verified examples where TEs contributed to expressed proteins. Our results are undoubtedly conservative but suggest that TEs may have contributed small protein segments to as many as 1.2% of all expressed, annotated A. thaliana genes.

Comparative genomic analysis reveals species-dependent complexities that explain difficulties with microsatellite marker development in molluscs

“…Specifically the non-autonomous TEs helitrons can capture and move gene fragments and are responsible for gene duplication and conversion (Morgante et al, 2005;Hollister and Gaut, 2007). This process can even lead to the formation of novel genes (Lockton and Gaut, 2009). Although Helitrons were not identified from the littorinids, the helitron DNAREP1_DYak was the second most highly abundant TE identified in G. cineraria.…”

Epigenetic Regulation of A Heat-Activated Retrotransposon in Cruciferous Vegetables

“…We aimed to analyze the phylogenetic relationships of the sequence variants, and to examine the lineages of the retrotransposons. The insertion of TEs indeed changed the local genome structure and could further interfere with the expression of the nearby genes [27]. Accordingly, the active TEs mostly have deleterious effects on their host, but specific insertions can rapidly proceed to fixation, when they are beneficial [28,29].…”

Transposable elements in Phyllostachys pubescens (Poaceae) genome survey sequences and the full-length cDNA sequences, and their association with simple-sequence repeats

“…There are relatively few TEs within the FL-cDNA sequences compared to the genome average (TEs represent 0.32% of FL-cDNAs but >20% of GSSs), which indicates that most TEs are not expressed in P. pubescens transcriptome due to the tight regulation of TEs (Jiao and Deng, 2007). However, the presence of TEs in and around genes appears to be essential for the growth and development of the host organism (Lockton and Gaut, 2009;Pritham, 2009), because they are involved in the regulation of gene expression (Marino-Ramirez et al, 2005;Feschotte, 2008). In a seminal study, Jordan et al (2003) reported that nearly 25% of experimentally characterized human promoters contain TE sequences, including empirically defined cis-regulatory elements.…”

“…Therefore, TEs may be responsible for the rate at which such incompatibility is generated in separated populations (Bennetzen, 2002). TEs are also essential components of the transcriptome during the growth and development of the host organism (Lockton and Gaut, 2009;Pritham, 2009). Transposase expression can be detected during tissue culture and growth under stress conditions, such as pathogen infection, pest infestation, drought, flooding, and exposure to radiation (Bennetzen, 2002;Jiao and Deng, 2007).…”