INFERRING COMPLEX GENOME ORGANIZATION FROM SELECTIVE LIBRARY METHODS

Texas A&M University, Genetics and Forest Science, College Station, Texas 77843-2135 USA

The large genome size of loblolly pine (Pinus taeda L.) is in part due to repetitive DNA (70 to 80%). The low-copy component is also excessive, and similar in size to the entire complex barley genome. It is estimated that roughly 1% of the pine low-copy component provides sequences necessary for gene expression. Selective library methods facilitate the study of interesting components of complex genomes. At the extreme end of the spectrum, cDNA libraries reduce the genome to only transcribed sequences, greater than a 99% reduction. Much more of the genome influences gene expression than simply the expressed sequences themselves. Selective methods that reduce the genome to a lesser extent are low-copy enriched libraries, with a predicted 70 to 80% reduction, and libraries of undermethylated DNA with further reduction. We have used both of these library approaches to reduce the loblolly pine genome. Comparing sequences from undermethylated versus low-copy libraries allows us to deduce the composition of the excess low-copy component. The frequency of trinucleotide repeats and retrotransposons are compared within the low-copy component, undermethylated component and total genome.