Comparative Genomics of Hardwood Tree Species Comparative Genomics of Hardwood Tree Species .
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Transcript of Comparative Genomics of Hardwood Tree Species Comparative Genomics of Hardwood Tree Species .
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 SequencingSpecies # 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 PopulationsHost 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 UniversityJohn Carlson, PITeodora Best, Research AssociateNicole Zembower, Technician Di Wu, PhD StudentNick Wheeler, Manager
University of Notre DameJeanne Romero-Severson, Co-PIDan Borkowski, PhD StudentArpita Konar, PhD StudentAndrea Noakes, PhD StudentLauren Fiedler, TechnicianOlivia Choudhary
Michigan Tech UniversityOliver Gailing, Co-PISandra Owusu, PhD StudentSudhir Khodwekar, PhD Student
University TennesseeScott Schlarbaum, Co-PIAmi Sharp, Research AssociateJason Hogan, Research AssociateJames Simons, Research Associate
Margaret Staton, Bioinformatics, Jack Davitt, Research AssociateNathan Henry, Research AssociateThomas Lane, Research Associate
University of MissouriMark Coggeshall, Co-PIChristopher Heim, MS student
Clemson UniversityHaiying Liang, Co-PIChris Saski, Director of CUGITatyana Zhebentyayev, Research Associate
Ketia Shumaker, Co-PI
Bert AbbottSteve DiFazioRobert MangoldRon SederoffDoug Soltis