comparative genomics of hardwood tree species comparative genomics of hardwood tree species

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





Fagaceae.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





www.hardwoodgenomics.org





Tulip Poplar

Sweetgum

Honeylocust

Northern Red Oak

Black Walnut

Sugar Maple

Blackgum

Green Ash





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





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





Genetic Map Construction

• Northern Red Oak• Black walnut

• Honeylocust

• Tulip poplar

• Green ash





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





General thoughts on Tripal and trees





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





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





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





CartograTree





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

comparative genomics of hardwood tree species comparative genomics of hardwood tree species

Documents

hardwood genomics database

hardwood trees current

caracter slide

phenotyping phenotyping

northern red oak 2341gb51

black walnut323

northern red oak339

black walnut3141gb78