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

• Published in: Tree genetics & genomes 2012-12, Vol.8 (6), p.1477-1485
• Main Authors: Lorenz, W. Walter, Ayyampalayam, Savavanaraj, Bordeaux, John M, Howe, Glenn T, Jermstad, Kathleen D, Neale, David B, Rogers, Deborah L, Dean, Jeffrey F. D
• Format: Article
• Language: English
• Subjects: Araucariaceae; Biomedical and Life Sciences; Biotechnology; cDNA libraries; complementary DNA; conifers; Cupressaceae; Datasets; ecological value; Ecosystem biology; Eucalyptus; expressed sequence tags; Forestry; Forests; Genes; Genetics; genome; Genomes; genotype; Genotypes; Gnetum gnemon; Life Sciences; Phylogenetics; Pine trees; Pinus taeda; Plant Breeding/Biotechnology; Plant Genetics and Genomics; Podocarpaceae; Populus; Resource development; Short Communication; Taxaceae; transcriptome; Tree Biology; Trees
• ISSN: 1614-2942; 1614-2950
• DOI: 10.1007/s11295-012-0547-y

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.