In silico characterization of microsatellites in Eucalyptus spp.: abundance, length variation and transposon associations

Abstract

This study assessed the abundance of microsatellites, or simple sequence repeats (SSR), in 19 Eucalyptus EST libraries from FORESTs, containing cDNA sequences from five species: E. grandis, E. globulus, E. saligna, E. urophylla and E. camaldulensis. Overall, a total of 11,534 SSRs and 8,447 SSR-containing sequences (25.5% of total ESTs) were identified, with an average of 1 SSR/2.5 kb when considering all motifs and 1 SSR/3.1 kb when mononucleotides were not included. Dimeric repeats were the most abundant (41.03%), followed by trimerics (36.11%) and monomerics (19.59%). The most frequent motifs were A/T (87.24%) for monomerics, AG/CT (94.44%) for dimerics, CCG/CGG (37.87%) for trimerics, AAGG/CCTT (18.75%) for tetramerics, AGAGG/CCTCT (14.04%) for pentamerics and ACGGCG/CGCCGT (6.30%) for hexamerics. According to sequence length, Class II or potentially variable markers were the most commonly found, followed by Class III. Two sequences presented high similarity to previously published Eucalyptus sequences from the NCBI database, EMBRA_72 and EMBRA_122. Local blastn search for transposons did not reveal the presence of any transposable elements with a cut-off value of 10 -50 . The large number of microsatellites identified will contribute to the refinement of marker-assisted mapping and to the discovery of novel markers for virtually all genes of economic interest.

Survey of simple sequence repeats in woodland strawberry (Fragaria vesca)

“…For example, (GT)n was found to be the most frequent repeat in mammals, whereas in plants and vertebrates, the dominant repeats were (AT)n and (CT)n, respectively (Lagercrantz et al, 1993;Paxton et al, 1996). Our results revealed that mononucleotide repeats were the most frequent SSRs in the F. vesca genome (such as A/T, representing 52.92% of total SSRs), followed by dinucleotide repeats (AT/TA, 14.43%), which is in stark contrast to results from previous studies (Cardle et al, 2000;Varshney et al, 2002;Rabello et al, 2005). This notable difference with previous results might be due to the fact that previous genome information was not complete, or that molecular hybridizations were the only methods previously available.…”

“…Here, 2 different patterns were observed with respect to the general relationship between the proportion of SSR lengths and the number of repeated units. First, there were well-defined decay curves when moving from trinucleotide to hexanucleotide repeats, and second, this trend was not observed in either mononucleotide or dinucleotide repeats, which is in concordance with the results of Varshney et al (2002) and Rabello et al (2005).…”

“…Class I repeats are highly polymorphic, but Class II repeats tend to be less variable (Temnykh et al, 2001). Class II SSRs were most commonly found in a study of 5 Eucalyptus species (Rabello et al, 2005). In addition, microsatellite primers are normally conserved within species and may even be transferable among different taxa (Yin et al, 2004;Castillo et al, 2008;Guan et al, 2012).…”

Mining of expressed sequence tag libraries of cacao for microsatellite markers using five computational tools

“…This is an agreement with genomic DNA analysis of Arabidopsis (Lawson and Zhang 2006), where A/T motifs were abundant among the monomer repeats in EST libraries. Similar results were also seen in eucalyptus (Rabello et al 2005) and in many other crop species (Gao et al 2003). In mycobacterial genomes stretches of long monomer repeats were noticed as they act as contingency loci (Sreenu et al 2007).…”

“…The estimated frequency of SSRs in cacao ESTs was one per 26.9 kb, based on the total size of the examined sequences (2616452 bp). The frequency of SSRs in ESTs of other crops reported earlier were one per 11.8 kb in rice; one per 23.8 kb in soybean, one per 17.24 kb in wheat and one per 28.32 kb in maize (Gao et al 2003) and one per 2.5 kb in eucalyptus (Rabello et al 2005). But the SSR frequency can follow a unique pattern in a plant species where seven-fold variation was seen in 24 plants of widely differing taxa with a mean of 114.7 SSRs per Mb (von Stackelberg et al 2006) with a standard deviation of +/− one per 60.1 Mb.…”