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

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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.

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Acknowledgments

This work was financially supported by Jiangsu Provincial Natural Science Foundation (BK2011871) and Natural Science Foundation of Jiangsu Academy of Forestry (Y0003). Special thanks are due to Dr. Siming Gan and anonymous reviewers for their valuable comments on the manuscript.

Conflict of interest

The authors declare that they have no conflict of interests.

Data archiving statement

All the 454 reads of S. babylonica and S. suchowensis were submitted to the sequence read archive (SRA) database at NCBI (http://www.ncbi.nlm.nih.gov/sra) with the accession number SRX389383 and SRX388824, respectively.

Author information

Correspondence to Xudong He.

Additional information

Communicated by P. Ingvarsson

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He, X., Zheng, J., Zhou, J. et al. Characterization and comparison of EST-SSRs in Salix, Populus, and Eucalyptus . Tree Genetics & Genomes 11, 820 (2015). https://doi.org/10.1007/s11295-014-0820-3

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Keywords

  • EST-SSR
  • Microsatellites
  • Salix
  • Populus
  • Eucalyptus