2187
Pine Genome Reference Sequence

The workshop will focus on the progress and applications of aspects of the Loblolly Pine Genome Project (aka PineRefSeq Project), a USDA-NIFA-funded project to produce reference genome sequences of three conifer species: loblolly pine (Pinus taeda), sugar pine (P. lambertiana), and Douglas-fir (Pseudotsuga menziesii).
Date: Saturday, January 11, 2014
Time: 8:00 AM-12:40 PM
Room: Pacific Salon 6-7 (2nd Floor)
Organizer:
Pat McGuire
Chair:
David Neale
8:00 AM
Break


8:15 AM
Welcome and Introduction


8:30 AM
Loblolly Pine Genome v1.0
Charles H. Langley, Department of Evolution and Ecology, University of California, Davis; Jill L. Wegrzyn, Department of Plant Sciences, Univ.of California-Davis; Kristian Stevens, Department of Evolution and Ecology, University of California, Davis; Aleksey Zimin, Institute for Physical Science and Technology, University of Maryland; Daniela Puiu, Johns Hopkins University, School of Medicine; Marc Crepeau, Department of Evolution and Ecology, University of California, Davis; Charis Cardeno, University of California, Davis; Maxim Koriabine, Children's Hospital Oakland Research Institute; Ann Holtz-Morris, Children's Hospital Oakland Research Institute; John Liechty, Department of Plant Sciences, University of California, Davis; Pedro J Martinez-Garcia, Department of Plant Sciences University of California; Hans Vasquez-Gross, University of California Davis; Brian Y. Lin, Department of Plant Sciences, Univ. of California-Davis; L. L. Zieve, Department of Plant Sciences, University of California; Matt Dougherty, University of California, Davis; S. Fuentes-Soriano, Department of Biology, Indiana University; L. Wu, National Center for Genome Analysis Support, Indiana University; D. Gilbert, Department of Biology, Indiana University; G. Marçais, Institute for Physical Sciences and Technology (IPST), University of Maryland; M. Roberts, .Institute for Physical Sciences and Technology (IPST), University of Maryland; C. Holt, Department of Human Genetics, University of Utah; M. Yandell, Department of Human Genetics, University of Utah; J.M. Davis, School of Forest Resources and Conservation; K. Smith, Southern Institute of Forest Genetics, USDA Forest Service; J.F.D. Dean, Warnell School of Forestry and Natural Resources, University of Georgia; W.W. Lorenz, Warnell School of Forestry and Natural Resources, University of Georgia; R.W. Whetten, Department of Forestry and Environmental Resources, North Carolina State University; R. Sederoff, Department of Forestry and Environmental Resources, North Carolina State University; Nicholas Wheeler, Pennsylvania State University; Pat McGuire, Department of Plant Sciences, University of California, Davis; Dorrie Main, Washington State University; Keithanne Mockaitis, Indiana University; Carol Loopstra, Texas A&M University; Pieter J. deJong, Children's Hospital Oakland Research Institute; James A Yorke, University of Maryland; Steven L Salzberg, Johns Hopkins University, School of Medicine; David Neale, Dept. Plant Sciences University of California Davis

9:00 AM
Annotation of the Lobolly Pine Megagenome
Jill Wegrzyn, University of Connecticut; John Liechty, Department of Plant Sciences, University of California, Davis; Kristian Stevens, Department of Evolution and Ecology, University of California, Davis; Carol Loopstra, Texas A&M University; Hans Vasquez-Gross, University of California Davis; Brian Lin, University of California, Davis; Matt Dougherty, University of California, Davis; Jacob Zieve, University of California, Davis; Pedro J Martinez-Garcia, Department of Plant Sciences University of California; Carson Holt, University of Utah; Mark Yandell, Eccles Institute of Human Genetics, University of Utah; Aleksey Zimin, Institute for Physical Science and Technology, University of Maryland; James A Yorke, University of Maryland; Marc Crepeau, Department of Evolution and Ecology, University of California, Davis; Daniela Puiu, Johns Hopkins University, School of Medicine; Steven L Salzberg, Johns Hopkins University, School of Medicine; Pieter J. deJong, Children's Hospital Oakland Research Institute; Keithanne Mockaitis, Indiana University; Dorrie Main, Washington State University; Chuck Langley, University of California, Davis; David Neale, Dept. Plant Sciences University of California Davis

9:30 AM
10:00 AM
Break


10:30 AM
Gene Expression in Conifers Revealed on a Comprehensive Scale:  Sequencing, Assembly and Classification of the Loblolly Pine Transcriptome
Keithanne Mockaitis, Indiana University; Le-Shin Wu, NCGAS, Indiana University; Carol Loopstra, Texas A & M University; Sara Fuentes-Soriano, Indiana University; Don Gilbert, Indiana University

10:50 AM
Recent Progress in the Shotgun Sequencing of Conifer Mega-Genomes
Kristian Stevens, Department of Evolution and Ecology, University of California, Davis; Marc Crepeau, Department of Evolution and Ecology, University of California, Davis; Pedro J Martinez-Garcia, Department of Plant Sciences University of California; Aleksey Zimin, Institute for Physical Science and Technology, University of Maryland; Daniela Puiu, Johns Hopkins University, School of Medicine; Maxim Koriabine, Children's Hospital Oakland Research Institute; Charis Cardeno, University of California, Davis; Ann Holtz-Morris, Children's Hospital Oakland Research Institute; Pieter J. deJong, Children's Hospital Oakland Research Institute; Steven L Salzberg, Johns Hopkins University, School of Medicine; James A Yorke, University of Maryland; Chuck Langley, University of California, Davis; David Neale, Dept. Plant Sciences University of California Davis

11:10 AM
Genetic Mapping of Scaffolds By Whole Genome Shotgun Sequencing
Pedro J Martinez-Garcia, Department of Plant Sciences University of California; Kristian Stevens, Department of Evolution and Ecology, University of California, Davis; Marc Crepeau, Department of Evolution and Ecology, University of California, Davis; John Liechty, Department of Plant Sciences, University of California, Davis; Charis Cardeno, University of California, Davis; Jill L. Wegrzyn, Department of Plant Sciences, Univ.of California-Davis; Charles H. Langley, Department of Evolution and Ecology, University of California, Davis; David Neale, Dept. Plant Sciences University of California Davis

11:30 AM
Assembly Improvements to Move Beyond Loblolly Pine Assembly v1.0
Aleksey Zimin, Institute for Physical Science and Technology, University of Maryland; Steven L Salzberg, Johns Hopkins University, School of Medicine; Daniela Puiu, Johns Hopkins University, School of Medicine; Kristian Stevens, Department of Evolution and Ecology, University of California, Davis; Michael Roberts, Univeristy of Maryland; James A Yorke, University of Maryland; Guillaume Marcais, Insitutte for Physical Science and Technology; Chuck Langley, University of California, Davis

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