Satellyptus: analysis and database of microsatellites from ESTs of Eucalyptus

Abstract

The main goal of our research was to search for SSRs in the Eucalyptus EST FORESTs database (using a software for mining SSR-motifs). With this objective, we created a database for cataloging Eucalyptus EST-derived SSRs, and developed a bioinformatics tool, named Satellyptus, for finding and analyzing microsatellites in the Eucalyptus EST database. The search for microsatellites in the FORESTs database containing 71,115 Eucalyptus EST sequences (52.09 Mb) revealed 20,530 SSRs in 15,621 ESTs. The SSR abundance detected on the Eucalyptus ESTs database (29% or one microsatellite every four sequences) is considered very high for plants. Amongst the categories of SSR motifs, the dimeric (37%) and trimeric ones (33%) predominated. The AG/CT motif was the most frequent (35.15%) followed by the trimeric CCG/CGG (12.81%). From a random sample of 1,217 sequences, 343 microsatellites in 265 SSR-containing sequences were identified. Approximately 48% of these ESTs containing microsatellites were homologous to proteins with known biological function. Most of the microsatellites detected in Eucalyptus ESTs were positioned at either the 5’ or 3’ end. Our next priority involves the design of flanking primers for codominant SSR loci, which could lead to the development of a set of microsatellite-based markers suitable for marker-assisted Eucalyptus breeding programs

Frequency and distribution of microsatellites from ESTs of citrus

“…Our study clearly illustrates that ESTs are a useful source of new SSR markers for citrus that are polymorphic and can be transferred between species and related genus. A number of reports have demonstrated that EST databases are a very good source of polymorphic markers for many organisms, including plants (Delseny et al, 1997;Scott et al, 2000;Kantety et al, 2002;Ceresini et al, 2005).…”

“…To identify the relative position of a SSR within a given sequence we used the strategy adapted by Ceresini et al (2005) that categorized the microsatellites as initial (I, close to the 5' end), middle (M) or end (E, close to the 3' end). Mononucleotides were excluded from this analysis.…”

“…This was initially limited to species where databanks existed, but the increase in available DNA sequence information, particularly ESTs (expressed sequence tags), has provided new opportunities for development of molecular markers for several annual and perennial plant species. Examples are available for Arabidopsis (Delseny et al, 1997), grape (Scott et al, 2000), cereals (Kantety et al, 2002), eucalyptus (Ceresini et al, 2005) and others. More recently in citrus, microsatellites were investigated and characterized from public EST-database (Chen et al, 2006;Dong et al, 2006).…”

In silico analysis of Simple Sequence Repeats from chloroplast genomes of Solanaceae species

“…SSRs were analyzed for type, abundance, and distribution (genic and intergenic regions). A total of 1,567 SSRs were identified, with an average frequency of 1.26 SSR per kb, which is a low EV Tambarussi et al frequency compared to the rice chloroplasts (6.5 SSR per kb) (Rajendrakumar et al 2007) and is higher when compared with Eucalyptus ESTs (0.37 SSR per kb) (Ceresini et al 2005) and Citrus ESTs (0.5 SSR per kb) (Palmieri et al 2007). This was expected since the occurrence of particular microsatellite motifs and repeats (especially the non-trimeric ones) could have implications on how the gene coding region is transcribed, due to risks of frameshift mutations (Metzgar et al 2000).…”

Characterization of chloroplast DNA microsatellites from Saccharum spp and related species

“…From a total of 1,785,569 bp that represents these plastomes, we identified 2427 cpSSRs, with an average frequency of 1.36 cpSSR per kb, which is higher than that of Eucalyptus ESTs (expressed sequence tags) (0.37 SSR per kb) (Ceresini et al, 2005) and Citrus ESTs (0.5 SSR per kb) (Palmieri et al, 2007). This was expected since the occurrence of particular microsatellite motifs and repeats (especially the non-trimeric ones) could have implications on how the gene coding region is transcribed due to risks of frameshift mutations (Metzgar et al, 2000).…”