title: Sequence of the Sugar Pine Megagenome.
abstract: 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 bp genome. It is the largest genome sequenced and assembled to date, and the first 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. Comparative analysis of P. lambertiana and P. taeda L. 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 candidate genes for resistance to this pathogen is of great ecological importance. The genome sequence 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 with Cr1 in unrelated sugar pine individuals sampled throughout the species' range, creating a solid foundation for future mapping. This genomic variation and annotated candidate genes characterized in our study of the Cr1 region are resources for future marker-assisted breeding efforts as well as for investigations of fundamental mechanisms of invasive disease and evolutionary response.
authors: Department of Evolution and Ecology, University of California at Davis, California 95616 kastevens@ucdavis.edu chlangley@ucdavis.edu.
authors: Kristian A
authors: KA
authors: Stevens
authors: Department of Ecology and Evolutionary Biology, University of Connecticut, Storrs, Connecticut.
authors: Jill L
authors: JL
authors: Wegrzyn
authors: Institute for Physical Sciences and Technology (IPST), University of Maryland, College Park, Maryland.
authors: Aleksey
authors: A
authors: Zimin
authors: Center for Computational Biology, McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University, Baltimore, Maryland.
authors: Daniela
authors: D
authors: Puiu
authors: Department of Evolution and Ecology, University of California at Davis, California 95616.
authors: Marc
authors: M
authors: Crepeau
authors: Department of Evolution and Ecology, University of California at Davis, California 95616.
authors: Charis
authors: C
authors: Cardeno
authors: Department of Ecology and Evolutionary Biology, University of Connecticut, Storrs, Connecticut.
authors: Robin
authors: R
authors: Paul
authors: Department of Ecology and Evolutionary Biology, University of Connecticut, Storrs, Connecticut.
authors: Daniel
authors: D
authors: Gonzalez-Ibeas
authors: Children's Hospital Oakland Research Institute, California.
authors: Maxim
authors: M
authors: Koriabine
authors: Children's Hospital Oakland Research Institute, California.
authors: Ann E
authors: AE
authors: Holtz-Morris
authors: Department of Plant Sciences, University of California at Davis, California.
authors: Pedro J
authors: PJ
authors: Martínez-García
authors: Department of Ecology and Evolutionary Biology, University of Connecticut, Storrs, Connecticut.
authors: Uzay U
authors: UU
authors: Sezen
authors: Institute for Physical Sciences and Technology (IPST), University of Maryland, College Park, Maryland.
authors: Guillaume
authors: G
authors: Marçais
authors: United States Department of Agriculture Forest Service, Pacific Southwest Research Station, Placerville, California.
authors: Kathy
authors: K
authors: Jermstad
authors: Department of Plant Sciences, University of California at Davis, California.
authors: Patrick E
authors: PE
authors: McGuire
authors: Department of Ecosystem Science and Management, Texas A&M University, College Station, Texas.
authors: Carol A
authors: CA
authors: Loopstra
authors: School of Forest Resources and Conservation, University of Florida, Gainesville, Florida.
authors: John M
authors: JM
authors: Davis
authors: Department of Biology, Virginia Commonwealth University, Richmond, Virginia.
authors: Andrew
authors: A
authors: Eckert
authors: Children's Hospital Oakland Research Institute, California.
authors: Pieter
authors: P
authors: de Jong
authors: Institute for Physical Sciences and Technology (IPST), University of Maryland, College Park, Maryland.
authors: James A
authors: JA
authors: Yorke
authors: Center for Computational Biology, McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University, Baltimore, Maryland.|Departments of Biomedical Engineering, Computer Science, and Biostatistics, Johns Hopkins University, Baltimore, Maryland.
authors: Steven L
authors: SL
authors: Salzberg
authors: Department of Plant Sciences, University of California at Davis, California.
authors: David B
authors: DB
authors: Neale
authors: Department of Evolution and Ecology, University of California at Davis, California 95616 kastevens@ucdavis.edu chlangley@ucdavis.edu.
authors: Charles H
authors: CH
authors: Langley
mesh_terms: D001487:Basidiomycota / Q000472:pathogenicity; D004251:DNA Transposable Elements; D014644:Genetic Variation; D059646:Genome Size; D018745:Genome, Plant; D028223:Pinus / Q000235:genetics* / Q000276:immunology / Q000382:microbiology; D057865:Plant Immunity / Q000235:genetics
chemical_list: D004251:DNA Transposable Elements
keywords: conifer genome; transposable elements; white pine blister rust