Sequence of the Sugar Pine Megagenome.

Until very recently, complete characterization of the megagenomes of conifers has remained elusive. The diploid genome of sugar pine ( Pinus lambertiana Dougl.) has a highly repetitive 31 billion base pair genome. With nearly 50% more DNA than the current record holder, Pinus taeda, sugar pine is the largest genome sequenced to date. This genome is the first to be sequenced from the subgenus Strobus , or white pines, a group that is notable for having the largest genomes among the pines. The genome represents a unique opportunity to investigate genome "obesity" in conifers and white pines. The crux of our sequencing approach has been to leverage aspects of conifer biology to reduce the complexity of the assembly problem. Comparative analysis of P. lambertiana and P. taeda reveals new insights on the conservation, age, and diversity of the highly abundant transposable elements, the primary factor determining genome size. Like most North American white pines the principal pathogen of P. lambertiana is white pine blister rust ( Cronartium ribicola J.C. Fischer ex Raben.). Identification of the candidate genes for resistance to this pathogen is great ecological importance. The genome afforded us the opportunity to make substantial progress on locating the major dominant gene for simple resistance hypersensitive response, Cr1 . We describe new markers and gene annotation that are both tightly linked to Cr1 in a mapping population and associated to Cr1 in unrelated individuals sampled throughout the range, creating a solid foundation for future mapping. This genomic variation and annotated candidate genes characterized in our study of Cr1 region are resources for future marker-assisted breeding efforts as well as investigations of fundamental mechanisms of invasive disease and evolutionary response.