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

Andrew Nunberg, Joseph A. Bedell, Mohammad A. Budiman, Robert W. Citek, Sandra W. Clifton, Lucinda Fulton, Deana Pape, Zheng Cai, Trupti Joshi, Henry Nguyen, Dong Xu, Gary Stacey

Research output: Contribution to journalArticle

6 Scopus citations

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.

Original languageEnglish
Pages (from-to)765-773
Number of pages9
JournalFunctional Plant Biology
Volume33
Issue number8
DOIs
StatePublished - Aug 8 2006
Externally publishedYes

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    Nunberg, A., Bedell, J. A., Budiman, M. A., Citek, R. W., Clifton, S. W., Fulton, L., Pape, D., Cai, Z., Joshi, T., Nguyen, H., Xu, D., & Stacey, G. (2006). Survey sequencing of soybean elucidates the genome structure, composition and identifies novel repeats. Functional Plant Biology, 33(8), 765-773. https://doi.org/10.1071/FP06106