Tree Genetics & Genomes

, Volume 3, Issue 3, pp 251–259 | Cite as

Characterization of EST-SSRs in loblolly pine and spruce

  • Yanik Bérubé
  • Jun Zhuang
  • Dainis Rungis
  • Steven Ralph
  • Jörg Bohlmann
  • Kermit Ritland
Original Paper

Abstract

In the first large study of conifer expressed sequence tag-simple sequence repeats (EST-SSRs), two large conifer EST databases were characterized for EST-SSRs. One database was from “interior spruce” (white and Engelmann spruce in Southern British Columbia) and Sitka spruce, while the other was from loblolly pine. We found 475 and 629 unique EST-SSRs in loblolly pine and spruce, respectively. 3′ ESTs contained 14% more SSRs than 5′ EST reads in loblolly pine and 41% more in spruce. Conifer EST-SSRs differed conspicuously from angiosperm EST-SSRs in several aspects. EST-SSRs were considerably less frequent in conifers (one EST-SSR every ∼50 kb) than in angiosperms (one EST-SSR every ∼20 kb). Dinucleotide repeats were the most abundant repeat class in conifers, while in angiosperms, trinucleotides were most common. Finally, the AT motif was the dominant motif recovered in both conifer species, whereas AG was the most common dinucleotide repeat in angiosperms. Also, as these EST-SSRs in conifers could be developed into useful genetic markers, our work demonstrates the value of large-scale EST sequencing projects for in-silico approaches for marker development.

Keywords

Expressed sequence tags Microsatellites Simple sequence repeats Conifers 

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Website references

  1. ftp://ftp.ncbi.nih.gov/repository/dbEST/; NCBI’s EST database ftp site
  2. http://www.genetics.forestry.ubc.ca/ritland/programs.html; Kermit Ritland’s repository of population genetics/bioinformatics programs. The Java program SSRFinder version 2 can be found here

Copyright information

© Springer-Verlag 2006

Authors and Affiliations

  • Yanik Bérubé
    • 1
  • Jun Zhuang
    • 1
  • Dainis Rungis
    • 1
  • Steven Ralph
    • 2
  • Jörg Bohlmann
    • 1
    • 2
  • Kermit Ritland
    • 1
  1. 1.Department of Forest SciencesUniversity of British ColumbiaVancouverCanada
  2. 2.Michael Smith LaboratoriesUniversity of British ColumbiaVancouverCanada

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