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Conifer DBMagic: a database housing multiple de novo transcriptome assemblies for 12 diverse conifer species

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Abstract

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 four million sequence reads that, along with available Sanger expressed sequence tags, were used to create contig assemblies using three different assembly algorithms: Newbler, MiraEST, and NGen. In addition, libraries from 11 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.

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Acknowledgments

The authors wish to acknowledge Yuan-Sheng Yu and Ujwal Bagal for their technical assistance. We also wish to thank Dr. Trevor Fenning for supplying the P. abies samples and Dr. Richard Cronn for early access to P. taeda chloroplast genome sequence information. These sequence data were produced by the US Department of Energy Joint Genome Institute http://www.jgi.doe.gov/ in collaboration with the user community. Particular thanks go to Christa Pennacchio, Kerrie Barry, Erika Lindquist, and their associates at JGI for directing cDNA library construction, 454 pyrosequencing, and some of the data filtering reported for this project. Partial funding for this work was provided by USDA/NRI CSREES CAP Award #2007-55300-18603.

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Authors and Affiliations

  1. Warnell School of Forestry and Natural Resources, University of Georgia, Athens, GA, 30602, USA

    W. Walter Lorenz, John M. Bordeaux & Jeffrey F. D. Dean

  2. Department of Plant Biology, University of Georgia, Athens, GA, 30602, USA

    Savavanaraj Ayyampalayam

  3. Department of Forest Ecosystems and Society, Oregon State University, Corvallis, OR, 97331, USA

    Glenn T. Howe

  4. USDA Forest Service, Pacific Southwest Research Station, Institute of Forest Genetics, Placerville, CA, 95667, USA

    Kathleen D. Jermstad

  5. Department of Plant Sciences, University of California, One Shields Avenue, Davis, CA, 95616, USA

    David B. Neale & Deborah L. Rogers

  6. Department of Biochemistry and Molecular Biology, Institute of Bioinformatics, University of Georgia, Athens, GA, 30602, USA

    Jeffrey F. D. Dean

Authors
  1. W. Walter Lorenz
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  2. Savavanaraj Ayyampalayam
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  3. John M. Bordeaux
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  4. Glenn T. Howe
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  5. Kathleen D. Jermstad
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  6. David B. Neale
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  7. Deborah L. Rogers
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  8. Jeffrey F. D. Dean
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Corresponding author

Correspondence to Jeffrey F. D. Dean.

Additional information

Communicated by R. Sederoff

Electronic supplementary material

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Supplementary File 1

Library and sequence metrics. This Excel file contains detailed information on the species and tissues used for each sequenced library, including tissue type, age of individual, library ID, cDNA priming, sequencing platform, number of plates sequenced, total reads, mean read length, SRA accession number, and genotype. Details of sample treatment and genotypes are provided on separate worksheets for the P. taeda, P. abies, P. lambertiana, and P. menziesii samples. (XLSX 17 kb)

Supplementary File 2

Assembly metrics. This Excel file contains detailed assembly metrics for all species assemblies and includes the number of input reads, total contigs, mean contig length, largest contigs, contigs ≥2 kb, contigs ≥1 kb, contigs ≥0.5 kb, and contigs having ≥5 ESTs. Metrics by Assembler are also shown on a second worksheet and include the percentage of bases assembled. (XLSX 16 kb)

Supplementary File 3

BLAST metrics. This Excel file contains BLASTX metrics for all species and all assemblies. The percentage of BLASTX hits determined after querying both the NCBI non-redundant and TAIR9 databases are shown for E-value cutoffs ≤1 × 10−5 and ≤1 × 10−15. Comparison of NCBI and TAIR9 returns by assembler are provided on a separate worksheet. (XLSX 17 kb)

Supplementary File 4

Tutorial on using the Conifer DBMagic database. This Powerpoint file guides users through the Conifer DBMagic database and its use to identify sequence assemblies of interest. (PPTX 2,052 kb)

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Lorenz, W.W., Ayyampalayam, S., Bordeaux, J.M. et al. Conifer DBMagic: a database housing multiple de novo transcriptome assemblies for 12 diverse conifer species. Tree Genetics & Genomes 8, 1477–1485 (2012). https://doi.org/10.1007/s11295-012-0547-y

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