Distribution of short interstitial telomere motifs in two plant genomes: putative origin and function

<p>Abstract</p> <p>Background</p> <p>Short interstitial telomere motifs (<it>telo </it>boxes) are short sequences identical to plant telomere repeat units. They are observed within the 5' region of several genes over-expressed in cycling cells. In synergy with various <it>cis</it>-acting elements, these motifs participate in the activation of expression. Here, we have analysed the distribution of <it>telo </it>boxes within <it>Arabidopsis thaliana </it>and <it>Oryza sativa </it>genomes and their association with genes involved in the biogenesis of the translational apparatus.</p> <p>Results</p> <p>Our analysis showed that the distribution of the <it>telo </it>box (AAACCCTA) in different genomic regions of <it>A. thaliana </it>and <it>O. sativa </it>is not random. As is also the case for plant microsatellites, they are preferentially located in the 5' flanking regions of genes, mainly within the 5' UTR, and distributed as a gradient along the direction of transcription. As previously reported in <it>Arabidopsis</it>, a conserved topological association of <it>telo </it>boxes with site II or TEF <it>cis</it>-acting elements is observed in almost all promoters of genes encoding ribosomal proteins in <it>O. sativa</it>. Such a conserved promoter organization can be found in other genes involved in the biogenesis of the translational machinery including rRNA processing proteins and snoRNAs. Strikingly, the association of <it>telo </it>boxes with site II motifs or TEF boxes is conserved in promoters of genes harbouring snoRNA clusters nested within an intron as well as in the 5' flanking regions of non-intronic snoRNA genes. Thus, the search for associations between <it>telo </it>boxes and site II motifs or TEF box in plant genomes could provide a useful tool for characterizing new cryptic RNA pol II promoters.</p> <p>Conclusions</p> <p>The data reported in this work support the model previously proposed for the spreading of <it>telo </it>boxes within plant genomes and provide new insights into a putative process for the acquisition of microsatellites in plants. The association of <it>telo </it>boxes with site II or TEF <it>cis</it>-acting elements appears to be an essential feature of plant genes involved in the biogenesis of ribosomes and clearly indicates that most plant snoRNAs are RNA pol II products.</p

SAT, a flexible and optimized Web application for SSR marker development

<p>Abstract</p> <p>Background</p> <p>Simple Sequence Repeats (SSRs), or microsatellites, are among the most powerful genetic markers known. A common method for the development of SSR markers is the construction of genomic DNA libraries enriched for SSR sequences, followed by DNA sequencing. However, designing optimal SSR markers from bulk sequence data is a laborious and time-consuming process.</p> <p>Results</p> <p>SAT (SSR Analysis Tool) is a user-friendly Web application developed to minimize tedious manual operations and reduce errors. This tool facilitates the integration, analysis and display of sequence data from SSR-enriched libraries.</p> <p>SAT is designed to successively perform base calling and quality evaluation of chromatograms, eliminate cloning vector, adaptors and low quality sequences, detect chimera or partially digested sequences, search for SSR motifs, cluster and assemble the redundant sequences, and design SSR primer pairs. An additional virtual PCR step establishes primer specificity. Users may modify the different parameters of each step of the SAT analysis.</p> <p>Although certain steps are compulsory, such as SSR motifs search and sequence assembly, users do not have to run the entire pipeline, and they can choose selectively which steps to perform. A database allows users to store and query results, and to redo individual steps of the workflow.</p> <p>Conclusion</p> <p>The SAT Web application is available at <url>http://sat.cirad.fr/sat</url>, and a standalone command-line version is also freely downloadable. Users must send an email to the SAT administrator <email>[email protected]</email> to request a login and password.</p