Characterization and comparison of EST-SSRs in Salix, Populus, and Eucalyptus

Abstract

Simple sequence repeats (SSRs) are molecular markers with great potential for plant genetic studies. With the development of high-throughput sequencing techniques, transcriptome sequencing projects provide valuable resources of expressed sequence tags (ESTs) for developing SSRs. To investigate the variation of EST-SSRs in different trees, three large EST databases of genera Salix, Populus, and Eucalyptus were compared for EST-SSR characteristics. The SSR-containing ESTs took account of 4.3, 8.4, and 12.2 % of the total number of ESTs for Salix, Populus, and Eucalyptus, respectively. The correlation between the repeat number and the motif type was negative, while that of the repeat number with the total SSR length or the number of SSRs was positive. Tri-nucleotide repeats were the most abundant motif type for Salix (47.7 %) and Eucalyptus (44.5 %), whereas di-nucleotide was the most common for Populus (38.8 %). The AG/CT repeat was the most abundant motif detected in all these trees. The most abundant tri- and tetra-nucleotide repeat motifs were AAG/CTT and AAAG/CTTT, respectively, for both Salix and Populus, while those were CCG/CGG and AGCG/CGCT for Eucalyptus. The EST-SSRs tended to occur in A/T-rich regions, and their repeat motif length appeared to decrease in variation with repeat numbers. These results may provide a deep insight into the characteristics of EST-SSRs in Salix, Populus, and Eucalyptus.