Skip to Main Content
U.S. Forest Service
Caring for the land and serving people

United States Department of Agriculture

Home > Search > Publication Information

  1. Share via EmailShare on FacebookShare on LinkedInShare on Twitter
    Dislike this pubLike this pub
    Author(s): W. Walter Lorenz; Savavanaraj Ayyampalayam; John M. Bordeaux; Glenn T. Howe; Kathleen D. Jermstad; David B. Neale; Deborah L. Rogers; Jeffrey F.D. Dean
    Date: 2012
    Source: Tree Genetics & Genomes (<em>Published online</em>) DOI 10.1007/s11295-012-0547-y
    Publication Series: Scientific Journal (JRNL)
    PDF: Download Publication  (0 B)


    Conifers comprise an ancient and widespread plant lineage of enormous commercial and ecological value. However, compared to model woody angiosperms, such as Populus and Eucalyptus, our understanding of conifers remains quite limited at a genomic level. Large genome sizes (10,000-40,000 Mbp) and large amounts of repetitive DNA have limited efforts to produce a conifer reference genome, and genomic resource development has focused primarily on characterization of expressed sequences. Here we report the completion of a conifer transcriptome sequencing project undertaken in collaboration with the U.S. DOE Joint Genome Institute that resulted in production of almost 12 million sequence reads. Five loblolly pine (Pinus taeda) cDNA libraries representing multiple tissues, treatments, and genotypes produced over 4 million sequence reads that, along with available Sanger expressed sequence tags (ESTs), were used to create contig assemblies using three different assembly algorithms: Newbler, miraEST, and NGen. In addition, libraries from eleven other conifer species, as well as one member of the Gnetales (Gnetum gnemon), produced 0.4 to 1.2 million sequence reads each. Among the selected conifer species were representatives of each of the seven phylogenetic families in the Coniferales: Araucariaceae, Cephalotaxaceae, Cupressaceae, Pinaceae, Podocarpaceae, Sciadopityaceae, and Taxaceae. Transcriptome builds for each species were generated using each of the three assemblers. All contigs for every species generated using each assembler can be obtained from Conifer DBMagic, a public database for searching, viewing, and downloading contig sequences, the associated sequence reads, and their annotations.

    Publication Notes

    • You may send email to to request a hard copy of this publication.
    • (Please specify exactly which publication you are requesting and your mailing address.)
    • We recommend that you also print this page and attach it to the printout of the article, to retain the full citation information.
    • This article was written and prepared by U.S. Government employees on official time, and is therefore in the public domain.


    Lorenz, W. Walter; Ayyampalayam, Savavanaraj; Bordeaux, John M.; Howe, Glenn T.; Jermstad, Kathleen D.; Neale, David B.; Rogers, Deborah L.; Dean, Jeffrey F.D. 2012. Conifer DBMagic: A database housing multiple de novo transcriptome assemblies for twelve diverse conifer species. Tree Genetics & Genomes (Published online) DOI 10.1007/s11295-012-0547-y.


    Google Scholar


    Coniferales, Pinus, transcriptome, database, annotation, gene models, comparative phylogenomics

    Related Search

    XML: View XML
Show More
Show Fewer
Jump to Top of Page