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
Comparative Genomics of
Hardwood Tree Species
http://www.hardwoodgenomics.org
Comparative Genomics of
Hardwood Tree Species
http://www.hardwoodgenomics.org
Fagaceae.org
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
Comparative Genomics of
Hardwood Tree Species
http://www.hardwoodgenomics.org
Comparative Genomics of
Hardwood Tree Species
http://www.hardwoodgenomics.org
www.hardwoodgenomics.org
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
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
TranscriptAndAnalysisModules
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
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
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
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
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
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 populationstructure and environmental associations to aridity across therange of loblolly pine
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 MurrellSERNEC -Southeastern Regional Network of Expertise and Collections
iDigBio
Comparative Genomics of
Hardwood Tree Species
http://www.hardwoodgenomics.org
Comparative Genomics of
Hardwood Tree Species
http://www.hardwoodgenomics.org
CartograTree
Comparative Genomics of
Hardwood Tree Species
http://www.hardwoodgenomics.org
Comparative Genomics of
Hardwood Tree Species
http://www.hardwoodgenomics.org
Comparative Genomics of
Hardwood Tree Species
http://www.hardwoodgenomics.org
Comparative Genomics of
Hardwood Tree Species
http://www.hardwoodgenomics.org
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 AssociateJason Hogan, Research AssociateJames 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 AbbottSteve DiFazioRobert MangoldRon SederoffDoug Soltis
