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This article in CS

  1. Vol. 52 No. 6, p. 2679-2686
     
    Received: Feb 1, 2012
    Published: October 10, 2012


    * Corresponding author(s): tmockler@danforthcenter.org
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doi:10.2135/cropsci2012.02.0065

Assembly and Characterization of the European Hazelnut ‘Jefferson’ Transcriptome

  1. Erik R. Rowleyab,
  2. Samuel E. Foxa,
  3. Douglas W. Bryantb,
  4. Christopher M. Sullivana,
  5. Henry D. Priestb,
  6. Scott A. Givanc,
  7. Shawn A. Mehlenbacherd and
  8. Todd C. Mockler *e
  1. a Dep. of Botany and Plant Pathology and Center for Genome Research and Biocomputing, Oregon State University, Corvallis, OR, 97331
    b The Donald Danforth Plant Science Center, 975 North Warson Road, St. Louis, MO, 63132
    c Informatics Research Core Facility, Molecular Microbiology and Immunology, University of Missouri, Columbia, MO, 65201
    d Dep. of Horticulture, Oregon State University, Corvallis, OR, 97331
    e Dep. of Botany and Plant Pathology and Center for Genome Research and Biocomputing, Oregon State University, Corvallis, OR, 97331, and The Donald Danforth Plant Science Center, 975 North Warson Road, St. Louis, MO, 63132. This work was supported by grants from the Oregon State University Agricultural Research Foundation and the Oregon Hazelnut Commission

Abstract

European hazelnut (Corylus avellana L.) is of worldwide agricultural significance, with breeding efforts focused on combining high nut yield and nut quality with resistance to diseases such as eastern filbert blight (EFB), a cause of severe crop loss in much of the United States. Oregon State University recently released a resistant cultivar, ‘Jefferson’ (OSU 703.007), that was chosen for transcriptome sequencing to establish further genomic resources for C. avellana L. We used Illumina ribonucleic acid sequencing (RNA-seq) to characterize complementary DNA (cDNA) libraries from four hazelnut tissues, including leaves, catkins, bark, and whole seedlings. The 6.8 Gb of hazelnut transcriptome data was assembled de novo into 28,255 contigs with an average length of 532 bp and an N50 (the minimum contig length necessary such that all contigs of equal or greater length will equal half of the bases of the assembly) of 961 bp. Sequence comparisons using BLASTX and gene ontology (GO) classifications were used to generate automated descriptive function annotations. High similarity of the predicted proteins to sequences in related plants demonstrates the validity of the transcript contigs, with 80.8% having similarity to grape (Vitis vinifera L.), poplar (Populus trichocarpa Torr. & A. Gray), and castor bean (Ricinus communis L.) sequences in the public domain. A survey of GO terms enriched among tissue-specific transcripts further validates the assembly. A basic local alignment search tool (BLAST) portal and web resources (http://hazelnut.cgrb.oregonstate.edu [accessed 8 Jan. 2010]) are available and will be of importance to breeders for marker-assisted breeding efforts.

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Copyright © 2012. Copyright © by the Crop Science Society of America, Inc.