Comparative Genomics of Hardwood Tree Species Comparative Genomics of Hardwood Tree Species The Hardwood Genomics Database: Current Status and Future Directions after Four Years of Resource Development Meg Staton

Comparative Genomics of Hardwood Tree Species Comparative Genomics of Hardwood Tree Species Fagaceae.org

Comparative Genomics of Hardwood Tree Species Comparative Genomics of Hardwood Tree Species 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 Comparative Genomics of Hardwood Tree Species

Comparative Genomics of Hardwood Tree Species Comparative Genomics of Hardwood Tree Species Tulip Poplar Sweetgum Honeylocust Northern Red Oak Black Walnut Sugar Maple Blackgum Green Ash

Comparative Genomics of Hardwood Tree Species Comparative Genomics of Hardwood Tree Species Transcriptome Sequencing Species# LibrariesRaw DataTranscripts Green Ash5585Gb107,611 Northern Red Oak 2341Gb51,662 Black Walnut3141Gb78,834 Black Gum166Gb55,630 Honeylocust52Gb56,845 Tulip Poplar285Gb53,346 Sweetgum4320Gb127,406 Sugar Maple6729Gb128,406 TOTAL268229Gb659,740 Transcript And Analysis Modules

Comparative Genomics of Hardwood Tree Species Comparative Genomics of Hardwood Tree Species Full Sibling Mapping Populations HostSpeciesNo. Seedlings Honeylocust226+ half sibs (149 full sibs so far) Northern Red Oak339 full sibs (confirmed) Black Walnut323 full sibs (confirmed) Tulip Poplar212 full sibs (controlled cross) Green Ash*328 full sibs (controlled cross) Replicated at different locations

Comparative Genomics of Hardwood Tree Species Comparative Genomics of Hardwood Tree Species Genetic Map Construction Northern Red Oak Black walnut Honeylocust Tulip poplar Green ash

Comparative Genomics of Hardwood Tree Species Comparative Genomics of Hardwood Tree Species Phenotyping Phenotyping in 2013, 2014 – leafing date – bud burst – leaf morphology – leaf N content Future phenotyping – stomatal density – insect defoliation – marcescence * php?page=pheno_caracter

Comparative Genomics of Hardwood Tree Species Comparative Genomics of Hardwood Tree Species General thoughts on Tripal and trees

Comparative Genomics of Hardwood Tree Species Comparative Genomics of Hardwood Tree Species 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 Comparative Genomics of Hardwood Tree Species 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

Comparative Genomics of Hardwood Tree Species Comparative Genomics of Hardwood Tree Species 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

Comparative Genomics of Hardwood Tree Species Comparative Genomics of Hardwood Tree Species CartograTree

Comparative Genomics of Hardwood Tree Species Comparative Genomics of Hardwood Tree Species

Comparative Genomics of Hardwood Tree Species Comparative Genomics of Hardwood Tree Species

Comparative Genomics of Hardwood Tree Species Comparative Genomics of Hardwood Tree Species 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