Survey sequencing of soybean elucidates the genome structure, composition and identifies novel repeats

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Contents Vol 33(8)

doi:10.1071/FP06106

Survey sequencing of soybean elucidates the genome structure, composition and identifies novel repeats

Andrew Nunberg ^A, Joseph A. Bedell ^A, Mohammad A. Budiman ^A, Robert W. Citek ^A, Sandra W. Clifton ^B, Lucinda Fulton ^B, Deana Pape ^B, Zheng Cai ^C, Trupti Joshi ^C ^D, Henry Nguyen ^E ^F, Dong Xu ^C ^D ^E, Gary Stacey ^D ^E ^F ^G ^H

^A Orion Genomics, LLC, 4041 Forest Park Ave, St Louis, MO 63108, USA.
^B Genome Sequencing Center, School of Medicine, Washington University, St Louis, MO 63130, USA.
^C Computer Science Department, University of Missouri, Columbia, MO 65211, USA.
^D Christopher S. Bond Life Sciences Center, University of Missouri, Columbia, MO 65211, USA.
^E National Center for Soybean Biotechnology, University of Missouri, Columbia, MO 65211, USA.
^F Division of Plant Science, University of Missouri, Columbia, MO 65211, USA.
^G Division of Biochemistry, Department of Molecular Microbiology and Immunology, University of Missouri, Columbia, MO 65211, USA.
^H Corresponding author. Email: staceyg@missouri.edu
^I This paper originates from a presentation at the Third International Conference on Legume Genomics and Genetics, Brisbane, Queensland, Australia, April 2006.





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Functional Plant Biology 33(8) 765–773 http://dx.doi.org/10.1071/FP06106
Submitted: 27 April 2006 Accepted: 24 May 2006 Published online: 2 August 2006

Abstract

In order to expand our knowledge of the soybean genome and to create a useful DNA repeat sequence database, over 24 000 DNA fragments from a soybean [Glycine max (L.) Merr.] cv. Williams 82 genomic shotgun library were sequenced. Additional sequences came from over 29 000 bacterial artificial chromosome (BAC) end sequences derived from a BstI library of the cv. Williams 82 genome. Analysis of these sequences identified 348 different DNA repeats, many of which appear to be novel. To extend the utility of the work, a pilot study was also conducted using methylation filtration to estimate the hypomethylated, soybean gene space. A comparison between 8366 sequences obtained from a filtered library and 23 788 from an unfiltered library indicate a gene-enrichment of ~3.2-fold in the hypomethylated sequences. Given the 1.1-Gb soybean genome, our analysis predicts a ~343-Mb hypomethylated, gene-rich space.