Insights Into The Loblolly Pine Genome: Characterization Of Fosmid Sequences

With the release of the preliminary assembly of Pinus taeda, it is of great importance to further define the repetitive content of the large and complex conifer genomes.  Recent investigations in loblolly pine have elucidated some of the genomic characteristics associated with the large genome size including rapid expansion of large retrotransposan families (Morse et al 2009; Kovach et al. 2010).  Here, we present a detailed analysis of the repeat content present in the current BAC and Fosmid sequence resources (102 and 90,976, respectively), including transposable elements (TEs), tandemly-arrayed sequences, and high copy number genes.  Tandem repeats were identified through the TRF (tandem repeat finder) and were calculated on the BAC and Fosmid sequence sets independently with estimates ranging from 2% to 3% of the genome.  Interspersed elements were evaluated with both similarity comparisons against the Repbase repeat repository and de novo analysis via the REPET pipeline.  Transposable elements (TEs) are abundant in the genome, representing between 20 and 30% of the sequence sets.  Retrotransposons are the most dominant class of TEs, accounting for approximately 17% of the genome and 80% of the repeat content.  LTR retrotransposons and more specifically, Gypsy, Copia, and Gymny families, constituted the largest sector of elements detected by similarity.  Analysis is underway to further characterize the approximately 12,000 unique de novo repeats identified via the REPET pipeline.  The resulting comprehensive repeat library represents an important resource to improve the assembly and facilitate the annotation of conifer genomes.