Hardwood Genomics Database (HGD): A Genomic and Genetic Web-Database for Hardwood Trees Research
Ming Chen
,
University of Tennessee, Knoxville, TN
Nate Henry
,
University of Tennessee, Knoxville, TN
Thomas Lane
,
University of Tennessee, Knoxville, Knoxville, TN
Nathaniel Cannon
,
Penn State University, University Park, PA
Mark Coggeshall
,
University of Missouri, Columbia, MO
Oliver Gailing
,
Michigan Technological University, Houghton, MI
Haiying Liang
,
Clemson University, Clemson, SC
Jeanne Romero-Severson
,
University of Notre Dame, Notre Dame, IN
Scott Schlarbaum
,
University of Tennessee, Knoxville, Knoxville, TN
Ketia Shumaker
,
The University of West Alabama, Livingston, AL
John E. Carlson
,
Penn State University, University Park, PA
Margaret Staton
,
University of Tennessee, Knoxville, TN
The Hardwood Genomics Database (HGD, www.hardwoodgenomics.org) is an integrated web-based database providing access to genomic and genetic data for 16 economically and phylogenetically important hardwood species. HGD contains assembled transcriptome sequences for eight species from several tree tissues and stress treatments such as ozone levels, cold, heat, drought and wounding. Low coverage whole genome sequences are available with in silico predicted genomic Simple Sequence Repeats (gSSRs) resources for ten species. The annotated genome reference sequence, targeted QTL sequences1 and genetically anchored physical map2 for Chinese Chestnut are also available. The web site provides access to online tools for mining and visualization of these data sets. Alignments, DNA/RNA variants and genome annotations for Chinese chestnut can be viewed using Jbrowse3, and users can annotate genes with the Apollo4 software tool. Syntenic relationships between Chinese chestnut and nine other plant organisms can be examined using SyMAP5. HGD also provides online BLAST for comparing sequences to transcriptome sequences or predicted proteins. Ongoing work includes development of an interface to the Galaxy data analysis platform6, integration of a gene expression viewer, a robust site-wide search function and additional RNASeq datasets.
1. Staton M, Zhebentyayeva T, Olukolu B, Fang GC, Nelson D, Carlson JE, Abbott AG: Substantial genome synteny preservation among woody angiosperm species: comparative genomics of Chinese chestnut (Castanea mollissima) and plant reference genomes. BMC Genomics 2015, 16:744.
2. Fang G-C, Blackmon BP, Staton ME, Nelson CD, Kubisiak TL, Olukolu BA, Henry D, Zhebentyayeva T, Saski CA, Cheng C-H: A physical map of the Chinese chestnut (Castanea mollissima) genome and its integration with the genetic map. Tree Genet Genomes 2012:1–13.
3. Skinner ME, Uzilov AV, Stein LD, Mungall CJ, Holmes IH: JBrowse: a next-generation genome browser. Genome Res 2009, 19:1630–1638.
4. Lee E, Helt GA, Reese JT, Munoz-Torres MC, Childers CP, Buels RM, Stein L, Holmes IH, Elsik CG, Lewis SE: Web Apollo: a web-based genomic annotation editing platform. Genome Biol 2013, 14:R93.
5. Soderlund C, Bomhoff M, Nelson WM: SyMAP v3. 4: a turnkey synteny system with application to plant genomes. Nucleic Acids Res 2011:gkr123.
6. Goecks J, Nekrutenko A, Taylor J, others: Galaxy: a comprehensive approach for supporting accessible, reproducible, and transparent computational research in the life sciences. Genome Biol 2010, 11:R86.
