Margaret Staton , University of Tennessee Institute of Agriculture, Knoxville, TN Nate Henry , University of Tennessee Institute of Agriculture, Knoxville, TN Mark Cook , University of Tennessee Institute of Agriculture, Knoxville, TN Thomas Lane , University of Tennessee Institute of Agriculture, Knoxville, TN Thomas Lane , University of Tennessee Institute of Agriculture, Knoxville, TN Jack Davitt , University of Tennessee Institute of Agriculture, Knoxville, TN Mark Coggeshall , University of Missouri, Columbia, MO Oliver Gailing , Michigan Technological University, Houghton, MI Haiying Liang , Clemson University, Clemson, SC Jeanne Romero-Severson , University of Notre Dame, Notre Dame, IN Scott Schlarbaum , University of Tennessee, Knoxville, TN Ketia Shumaker , The University of West Alabama, Livingston, AL Nicholas Wheeler , Pennsylvania State University, Centralia, WA John E. Carlson , Pennsylvania State University, University Park, PA Forests and trees provide essential ecosystem services as well as critical industrial and economic value for society. Faced with pressures from climate change, invasive insects and habitat destruction from human activity, there is a growing need for tools and resources for more efficient tree management and improvement efforts in both natural forests and plantations. The Hardwood Genomics database is an online community website for hardwood tree genomics and genetics resources (hardwoodgenomics.org). It provides access to (a) integrated and curated datasets including transcriptomes, genomes, genetic maps, QTL maps, population resources, and phenotypes, (b) online tools to perform custom analysis and visualization of those data sets , and (c) outreach activities, presentations and progress reports to inform stakeholders of current research efforts and coming scientific resources.The site is built with the open source software package Tripal (Ficklin et al., 2011) and also utilizes the data visualization software packages Gbrowse (Stein, 2013), Symap (Soderlund et al., 2011) and CMap (Youens-Clark et al., 2009). Future development will include continued expansion to include more public data sets, introducing Tripal software innovations from other groups to our database and developing web services to promote database interoperability.This project is supported by grant # TRPGR IOS-1025974 from the National Science Foundation’s Plant Genome Research Program.

1. Comparative Genomics of
Hardwood Tree Species
http://www.hardwoodgenomics.org
Comparative Genomics of
Hardwood Tree Species
http://www.hardwoodgenomics.org
The Hardwood Genomics Database: Current
Status and Future Directions after Four Years
of Resource Development
Meg Staton

2. Comparative Genomics of
Hardwood Tree Species
http://www.hardwoodgenomics.org
Comparative Genomics of
Hardwood Tree Species
http://www.hardwoodgenomics.org
Fagaceae.org

3. Comparative Genomics of
Hardwood Tree Species
http://www.hardwoodgenomics.org
Comparative Genomics of
Hardwood Tree Species
http://www.hardwoodgenomics.org
Comparative Genomics of Environmental Stress
Responses in North American Hardwoods
• February 1, 2011 – January
31, 2015
• Creating genomic resources
for hardwood trees
• Current and increasingly
devastating forest threats:
invasive pests and pathogens,
climate change
• Enable population,
evolutionary and
conservation genetics

4. Comparative Genomics of
Hardwood Tree Species
http://www.hardwoodgenomics.org
Comparative Genomics of
Hardwood Tree Species
http://www.hardwoodgenomics.org
www.hardwoodgenomics.org

5. Comparative Genomics of
Hardwood Tree Species
http://www.hardwoodgenomics.org
Comparative Genomics of
Hardwood Tree Species
http://www.hardwoodgenomics.org
Tulip Poplar
Sweetgum
Honeylocust
Northern Red Oak
Black Walnut
Sugar Maple
Blackgum
Green Ash

6. Comparative Genomics of
Hardwood Tree Species
http://www.hardwoodgenomics.org
Comparative Genomics of
Hardwood Tree Species
http://www.hardwoodgenomics.org
Transcriptome Sequencing
Species # Libraries Raw Data Transcripts
Green Ash 55 85Gb 107,611
Northern
Red Oak
23 41Gb 51,662
Black Walnut 31 41Gb 78,834
Black Gum 16 6Gb 55,630
Honeylocust 5 2Gb 56,845
Tulip Poplar 28 5Gb 53,346
Sweetgum 43 20Gb 127,406
Sugar Maple 67 29Gb 128,406
TOTAL 268 229Gb 659,740
Transcript
And
Analysis
Modules

7. Comparative Genomics of
Hardwood Tree Species
http://www.hardwoodgenomics.org
Comparative Genomics of
Hardwood Tree Species
http://www.hardwoodgenomics.org
Full Sibling Mapping Populations
Host Species No. Seedlings
Honeylocust 226+ half sibs (149 full sibs so far)
Northern Red Oak 339 full sibs (confirmed)
Black Walnut 323 full sibs (confirmed)
Tulip Poplar 212 full sibs (controlled cross)
Green Ash* 328 full sibs (controlled cross)
Replicated at
different
locations

8. Comparative Genomics of
Hardwood Tree Species
http://www.hardwoodgenomics.org
Comparative Genomics of
Hardwood Tree Species
http://www.hardwoodgenomics.org
Genetic Map Construction
• Northern Red Oak
• Black walnut
• Honeylocust
• Tulip poplar
• Green ash

9. Comparative Genomics of
Hardwood Tree Species
http://www.hardwoodgenomics.org
Comparative Genomics of
Hardwood Tree Species
http://www.hardwoodgenomics.org
Phenotyping
• Phenotyping in 2013, 2014
– leafing date
– bud burst
– leaf morphology
– leaf N content
• Future phenotyping
– stomatal density
– insect defoliation
– marcescence
*http://w3.pierroton.inra.fr/CartoChene/index.
php?page=pheno_caracter

10. Comparative Genomics of
Hardwood Tree Species
http://www.hardwoodgenomics.org
Comparative Genomics of
Hardwood Tree Species
http://www.hardwoodgenomics.org
General thoughts on Tripal and trees

11. Comparative Genomics of
Hardwood Tree Species
http://www.hardwoodgenomics.org
Comparative Genomics of
Hardwood Tree Species
http://www.hardwoodgenomics.org
Trees – Special Genomic/Genetic Characters
• The special case of the
conifers - Giant genomes
– Pinerefseq Project (David
Neale, Jill Wegrzyn)
– 19Gb douglas fir
– 22Gb loblolly pine
– 33.5Gb sugar pine
• High heterozygosity
• Ontology expansion,
pathway maps expansion

12. Comparative Genomics of
Hardwood Tree Species
http://www.hardwoodgenomics.org
Comparative Genomics of
Hardwood Tree Species
http://www.hardwoodgenomics.org
Trees improvement/conservation
• Less traditional breeding
– Long generation time
– Lots of space
– Difficult – not
domesticated, tall
• Less clonal propagation –
labor intensive
• Whole genome selection
– Improved selection
• Association genetics
Eckert et al 2010 Patterns of population
structure and environmental associations to aridity across the
range of loblolly pine

13. Comparative Genomics of
Hardwood Tree Species
http://www.hardwoodgenomics.org
Comparative Genomics of
Hardwood Tree Species
http://www.hardwoodgenomics.org
Trees as part of forest ecosystems
• Landscape genomics
– GIS, maps
– Phenotype x genotype x environment
• Broader perspectives
– Ecosystem services
– Microbial associations
– Similar to ecological model plants
• Herbarium samples are being obtained for all
parent trees
• vouchers will be deposited at the Dunn-
Palmer Herbarium at MU
• imaged and uploaded to the TROPICOS
website
Zach Murrell
SERNEC -
Southeastern Regional
Network of Expertise and
Collections
iDigBio

14. Comparative Genomics of
Hardwood Tree Species
http://www.hardwoodgenomics.org
Comparative Genomics of
Hardwood Tree Species
http://www.hardwoodgenomics.org
CartograTree

15. Comparative Genomics of
Hardwood Tree Species
http://www.hardwoodgenomics.org
Comparative Genomics of
Hardwood Tree Species
http://www.hardwoodgenomics.org

16. Comparative Genomics of
Hardwood Tree Species
http://www.hardwoodgenomics.org
Comparative Genomics of
Hardwood Tree Species
http://www.hardwoodgenomics.org

17. Comparative Genomics of
Hardwood Tree Species
http://www.hardwoodgenomics.org
Comparative Genomics of
Hardwood Tree Species
http://www.hardwoodgenomics.org
NSF Advisory Board
Penn State University
John Carlson, PI
Teodora Best, Research Associate
Nicole Zembower, Technician
Di Wu, PhD Student
Nick Wheeler, Manager
University of Notre Dame
Jeanne Romero-Severson, Co-PI
Dan Borkowski, PhD Student
Arpita Konar, PhD Student
Andrea Noakes, PhD Student
Lauren Fiedler, Technician
Olivia Choudhary
Michigan Tech University
Oliver Gailing, Co-PI
Sandra Owusu, PhD Student
Sudhir Khodwekar, PhD Student
University Tennessee
Scott Schlarbaum, Co-PI
Ami Sharp, Research Associate
Jason Hogan, Research Associate
James Simons, Research Associate
Margaret Staton, Bioinformatics,
Jack Davitt, Research Associate
Nathan Henry, Research Associate
Thomas Lane, Research Associate
University of Missouri
Mark Coggeshall, Co-PI
Christopher Heim, MS student
Clemson University
Haiying Liang, Co-PI
Chris Saski, Director of CUGI
Tatyana Zhebentyayev, Research
Associate
Ketia Shumaker, Co-PI
Bert Abbott
Steve DiFazio
Robert Mangold
Ron Sederoff
Doug Soltis