me Publications Presentations TreeGenes

Summary of PineRefSeq…
Rationale
Conifer genomes present challenges for successful sequencing, mainly due to their large size and complexity. To address these challenges, we have assembled a research team with the requisite expertise and experience having elicited and productively used prior federal support for research on loblolly pine genetic diversity, development of conifer genetic and genomic resources, development of molecular markers for complex traits, development of the bioinformatics and database infrastructure used by a majority of conifer genetics researchers today, development and extension of marker-informed conifer breeding, and development of many of the bioinformatics data display, analysis, and storage software and algorithms in use today.

Goal
Development of a high quality reference genome sequence for loblolly pine, Douglas-fir and sugar pine by means that can serve as a model approach for sequencing other large, complex genomes and empower the forest tree biology research community and the broader biological research community in the practical use and application of this resource.

Specific Aims
High-quality reference genome sequences of loblolly pine, Douglas-fir and sugar pine
Transcriptome sequencing for gene discovery, reference building, and aids to genome assembly
Dendrome and TreeGenes databases: Annotation, data integration, and distribution

Guiding Principles
EMPOWERMENT. Our goal is to develop the technologies, platforms and bioinformatics infrastructures to rapidly and inexpensively sequence large and complex genomes of coniferous forest trees. This will allow the forestry community to begin sequencing the many genomes of economic and ecological importance without a dependence on centralized genome centers.
ADAPTIVE. We recognize the sequencing technologies are developing rapidly and that we must have the expertise and flexibility to rapidly adopt new approaches into our overall sequencing strategy.
COMPARATIVE. We recognize the power of comparative genomics approaches in assembling and annotating genome sequences and will use this approach throughout the project.
OPEN ACCESS. We have a policy of sharing all data generated from this project with the research community

Impact and Outcomes
Our project will achieve broad community empowerment through the development of a reference conifer genome sequence. Short-term impacts include facilitating genomic-based breeding for wood products and energy, developing diagnostic tools to estimate risk and impacts caused by changing environments, and facilitating genome sequencing in other conifers. Additional outcomes and longer-term impacts include more complete integration of forest and horticultural tree genome projects and integration with other areas of tree biology (e.g., via the NSF iPlant Tree Biology Cyberinfrastructure initiative).

Species To Be Sequenced…

Members…

Collaborations…
USDA FS: Douglas-fir Transcriptome Observatory for the Pacific Northwest
Richard Cronn, USFS PNWRS, Corvallis OR
USDA FS: Sugar pine transcriptome project
Jessica Wright, USFS PSWRS, Davis CA
Sweden: Norway Spruce Genome Project
Par Ingvarsson, Umea Plant Science Centre
Canada: SMarTForest: Spruce Marker Technologies for Sustainable Forestry
Kermit Ritland, University of British Columbia, Vancouver BC
Canada: AdapTree: Assessing the Adaptive Portfolio of Reforestation Stocks for Future Climates, Genome Canada
Sally Aitken, University of British Columbia, Vancouver BC
Europe: ProCoGen
Carmen Diaz-Sala, University of Alcala, Madrid, Spain
Maria-Teresa Cevera, INIA-CIFOR, Madrid, Spain
Russia: Siberian Conifer Genome Project
Siberian Federal University, Krasnoyarsk 660036, Russia
In The News…
UC Davis Researchers Sequence California Sugar Pine Genome
Sequencing Sugar Pine Genome, Transcriptome Offer Glimpse into Evolution of Oversized Genomes
Loblolly Genome Press Coverage
Norway Spruce Genome Sequenced: Largest Ever to Be Mapped
Giant genomes felled by DNA sequencing advances
Review of Steven Salzberg’s presentation at CSHL
Steven Salzberg wins the 2013 Benjamin Franklin Award!
USDA-Funded Research Leads to Initial Draft of the Loblolly Pine Genome
Huge DNA Code of the Christmas Tree Being Revealed
USDA Grants $40M to UC-Davis
UC Davis wins ag research grants
Plant scientists receive $40 M to lead multistate ag programs
Forestry + genetics = a blister rust solution?
New Forest Biology Research Center opens at UC Davis
Nurturing a rare breed
Data Releases…
Data Use Policy
Pinus taeda assembly v2.0
Pinus taeda assembly v1.01
Pinus taeda mitochondrial genome
Pinus taeda assembly v1.0
Pseudotsuga menziesii assembly v1.0
Pseudotsuga menziesii assembly v0.5
Pinus lambertiana assembly v1.5
Pinus lambertiana assembly v1.0
Pinus lambertiana assembly v0.5
Publications…
Zimin et al: An improved assembly of the loblolly pine mega-genome using long-read single-molecule sequencing
Gonzalez-Ibeas et al: Assessing the Gene Content of the Megagenome: Sugar Pine (Pinus lambertiana)
Stevens et al: Sequence of the Sugar Pine Megagenome
Neale et al : Decoding the massive genome of loblolly pine using haploid DNA and novel assembly strategies
Zimin et al : Sequencing and Assembly of the 22-Gb Loblolly Pine Genome
Wegrzyn et al : Unique Features of the Loblolly Pine (Pinus taeda L.) Megagenome Revealed Through Sequence Annotation
Wegrzyn et al : Insights into the Loblolly Pine Genome: Characterization of BAC and Fosmid Sequences
Outreach Presentations…
Reference Genome Sequencing: Conifer Genomics
Introduction to PineRefSeq 2012
Presentations at Plant and Animal Genome Conference
Pinus taeda Genomics Projects…
Allele Discovery of Economic Pine Traits (ADEPT)
Allele Discovery of Economic Pine Traits 2 (ADEPT2)
241,796 reads submitted to Trace Archive
6,178 amplicons to the PopSets repository via tbl2asn program
10 BAC sequences were submitted to Genbank (GU477256 – GU477266)
Conifer Comparative Genomics Project (CCGP)
Conifer Translational Genomics Network (CTGN)
Forest Tree Genetic Stock Center (FTGSC)
Accelerating Pine Genomics – MGEL
92 BAC sequences were submitted to Genbank (AC241263_1 – AC241362_1)
Expanded EST Resource for Pines and Other Conifers

Douglas-fir Genomics Projects…
Douglas-fir Genome Project
ADAPT
Agenda2020
Douglas-fir Transcriptome Observatory

White Pine Genomics Projects…
White Pine Genome Project
Strobusphere

Funding…
Funding for the Loblolly Pine Genome Project is provided by: USDA/NIFA #2011-67009-30030