APG has performed a Cot analysis of the loblolly pine genome.  The results of this analysis are currently being prepared for publication.  However, initial findings presented at Plant & Animal Genome XIV can be seen on one of our posters from that meeting (click here to see poster).

What is Cot analysis?  For several years now, the term “genomics” has been a “buzz word” in the scientific community.  However, the first detailed, comparative investigations of genomes (arguably the first genomic experiments) were performed roughly 35 years before scientists, academic departments, and scientific institutes started using the “genomics” moniker.  In the 1960s, Roy Britten and his colleagues began investigating the renaturation kinetics of genomic DNA in solution using a technique they called “Cot analysis”.  In a Cot analysis, the compound hydroxyapatite (HAP) is used to preferentially separate renatured (double-stranded) DNA from single-stranded DNA.  A review of the steps in a Cot analysis (updated to include new technologies as described in Peterson et al. 1998) is shown in the PDF tutorial Cot Analysis, Cot Filtration, and Cot-Based Cloning & Sequencing.  From a Cot analysis one can determine genome size, the fraction of single-copy DNA in a genome, and the number, size, complexity, and relative arrangement (dispersed vs. tandem arrays) of repetition-based DNA components.  Likewise, Cot analysis allows many of the basic characteristics of genomes to be compared between genetically similar/dissimilar organisms.  With the advent of molecular cloning techniques, most genome researchers abandoned the notoriously difficult business of Cot analysis.  However, the principles of nucleic acid hybridization developed through Cot research form the basis of many molecular biology techniques, and information generated in Cot studies remains central to current knowledge of genome structure.