35th NPS abstract book

Computational tools and resources for comparative
tree genomics
S4.2
JILL WEGRZYN 1,2 , EMILY GRAU 3 , HANS VASQUEZ- 15:30–16.00
GROSS 3 , TAEIN LEE 4, JODI HUMANN 4 , STEPHEN FICKLIN 4 ,
MARGARET STATON 5 , NATHAN HENRY 5 , DOREEN MAIN 4
and DAVID NEALE 3
jill.wegrzyn@uconn.edu
1 Department of Ecology and Evolutionary Biology, University of
Connecticut, Storrs, CT, USA; 2 Institute for Systems Genomics, University of
Connecticut, Storrs, CT, USA; 3 Department of Plant Sciences, University of
California at Davis, Davis, CA, USA; 4 Department of Horticulture,
Washington State University, Pullman, WA, USA; 5 Department of
Entomology and Plant Pathology, University of Tennessee, TN, USA
Full genome sequences are being generated for the first time for several conifer and hardwood
species. The recent influx of genomic resources from previously underserved tree species presents a
wealth of information and scientific opportunities to the research community. Recipients of this data
are often faced with navigating the complex landscape of online resources with conflicting genome
versions, incomplete annotations, and various levels of resolution. As is often the case with early
genome sequences and genomic sets that pre-date a full genome, the optimal data source and
associated metadata are difficult to obtain. This problem is magnified by the size of genomic
datasets which produce additional barriers once the user brings this information to a desktop
machine for analysis. In addition to genomic data, we are increasingly interested in associating
phenotypic and environmental metrics to geo-referenced trees. These datasets provide additional
computational challenges and reside in repositories even more diverse than those holding genomic
artefacts.
Here, we will describe two clade organism databases – TreeGenes
(http://dendrome.ucdavis.edu/treegenes) and the Hardwood Genomics Web
(http://www.hardwoodgenomics.org/). Aside from direct access to curated genomic resources, we
present two tools – GenSAS and CartograTree. GenSAS is a genome visualization tool that supports
moderate to large genome assemblies and guides researchers through the process of repeat
identification, gene prediction, structural annotation, and comparative genomics. CartograTree is an
interactive workspace that allows for geographical visualization and engagement of high
performance computing (HPC) resources. CartograTree merges genomic, phenotypic, and
environmental data to facilitate association studies in a variety of forest trees.
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