HarvEST:Barley and the Affymetrix Barley1 GeneChip
Harvest:Barley includes the information that was the basis of the Affymetrix "Barley1" microarray chip content described in Close et al. (2004) and Close (2005). HarvEST:Barley (version 1.65; 556 MB Windows installation file or online version) contains special features for viewing the chip content. This includes updated and extended gene annotations, and export tools so that this information can be integrated into users' local databases. Development of HarvEST:Barley has been supported by the USDA Plant Genome program and the NSF Plant Genome Research Program.
Close TJ, Wanamaker S, Caldo RA, Turner SM, Ashlock DA, Dickerson JA, Wing RA, Muehlbauer GJ, Kleinhofs A, Wise RP. 2004. A new resource for cereal genomics: 22K barley GeneChip comes of age. Plant Physiology 134: 960-968.
Close TJ. 2005. The barley microarray: a community vision and application to abiotic stress. Czech Journal of Genetics and Plant Breeding 41: 144-152.
The Barley1 GeneChip is the Product of Worldwide Cooperation
The Barley1 GeneChip was the culmination of a vision and cooperation of the worldwide barley community. Barley EST sequences (approximately 400,000) were gathered from worldwide colleagues by Timothy Close at the University of California, Riverside. Colleagues at Iowa State University (Dan Ashlock, Roger Wise) parsed about 1000 additional sequences from the GenBank nr database and provided several sequence related to a region of the barley genome containing a Blumeria resistance gene. Additional colleagues proposed transgene sequences. EST sequence data were processed by Wanamaker and Close using phred, cleaned of vector & cloning system oligos using cross_match, scanned with BLAST to identify and remove rRNA clones and various contaminating sequences, then assembled. The sequence assemblies in HarvEST:Barley were produced using MegaBLAST followed by CAP3 using TIGRs TGICL management tool by Steve Wanamaker at the University of California, Riverside. Chimeras were removed by Close, Wanamaker and Jan Svensson (University of California, Riverside) using semi-automated inspection of contigs and singletons. Following this process, additional sequences related to possible transgenes were added to the chip content. Representative sequences (exemplars) were then transmitted by Wanamaker and Close to Affymetrix for oligo design. The chip was produced as part of the USDA-IFAFS project, "An Integrated Physical and Expression Map of Barley for Triticeae Improvement". A more detailed list of those in the barley community who contributed to chip content is given below.
Excerpt from "The Barley Microarray. A Community Vision and Application to Abiotic Stress", International Barley Genetics Symposium, Brno, Czech Republic, June 2004 with one addition (Australia) and Czech Journal of Genetics and Plant Breeding 41:144-152 (2005).
Most of the EST data contributors and their barley EST projects are cited below.
· Clemson University Genomics Institute, Clemson, South Carolina, USA: Rod Wing and Dorrie Main, with EST production support from Dilara Begum, David Frisch, Michael Atkins, Yeisoo Yu, D. Henry, M. Palmer, T. Rambo, J. Simmons and R. Oates. Supported by the United States Department of Agriculture – National Research Initiative project, “Establishment of a Genetically and Physically Anchored EST Resource for Barley Genomics” (Andris Kleinhofs, PI; Rod Wing, Timothy Close, Roger Wise).
· Institute of Plant Genetics and Crop Plant Research (IPK), Gatersleben, Germany: Andreas Graner, Nils Stein and Winfriede Weschke with support from Hangning Zhang, Elena Potokina, Volodya Radchuck and Jelena Perovic. Barley ESTs from the project "Partial Sequencing of cDNAs for the Generation of Expressed Sequence Tags (ESTS) of Barley" funded by the state of Saxony-Anhalt. Libraries and funding for these ESTs also provided by the project "An Expressed Sequence Tagged (EST) database of barley" (Andreas Graner and Peter Landrigde PIs), funded by the Grains Research and Development Corporation, Government of Australia.
· Okayama University, Japan: Kazuhiro Sato, Daisuke Saisho and Kazuyoshi Takeda. National Institute of Genetics, Japan: Yuji Kohara and Tadasu Shin-i. ESTs from the collaborative project between the Barley Germplasm Center, Okayama University and Center for Genetic Resource Information, National Institute of Genetics. This project has been supported by a Grant-in-aid for Scientific Research on Priority Areas C from the Ministry of Education, Culture, Sports, Science and Technology (MEXT) of Japan and by CREST (Core Research for Evolutional Science and Technology) of JST (Japan Science and Technology Corporation).
· Scottish Crop Research Institute (SCRI), Invergowrie, Dundee, Scotland, UK: Robbie Waugh, Peter Hedley, H. Liu, D. Caldwell, Luke Ramsay, David Marshall, and Linda Cardle. Developed as part of the barley transcriptome resources of BBSRC/SEERAD funded cereal ‘Investigating Gene Function’ project.
· Hans Bohnert (USA), Dept. Biochemistry and Molecular Biophysics, University of Arizona, Tucson, AZ 85721, and Plant Sciences and Dept. Crop Sciences, University of Illinois, Urbana-Champaign, IL, 61801. Supported by NSF – Plant Genome Program (98-13360); data collected by: N.Z. Ozturk, C.B. Michalowski, S. Brazille, C. Borchert, C. Palacio, C. Normand, C. Murphy, R. Kelley, S.A. Sant, H. McLaughlin, and M.A. Fredricksen.
· Institute of Biotechnology, University of Helsinki, Helsinki, Finland and MTT Agrifood Research, Jokioinen, Finalnd: Alan Schulman, Ari-Matti Sarén, Jaakko Tanskanen, and Lars Paulin with support from Tanja Horko and Ursula Lönnqvist. ESTs from the project, “Production of EST tools for barley gene discovery and exploitation” funded by major contributions of TEKES, the National Technology Agency of Finland, and Boreal Plant Breeding Ltd., as well as by contributions from Polttimo Companies Ltd. and the Raisio Group, Ltd. Additional in-kind contributions from CSC- Scientific Computing Ltd. and Visipoint OY.
In addition, Dan Ashlock at Iowa State University extracted complete barley cDNA and gene sequences from the National Center for Biotechnology “nr” database, and David Matthews, head curator of GrainGenes at Cornell University, provided sequences from Gottfried Kuenzel (IPK Gatersleben) that were available only from the GrainGenes database (http://wheat.pw.usda.gov/cgi-bin/graingenes/browse.cgi). The final sequences represented on the chip included commonly used transgenes suggested by Peggy Lemaux and Shibo Zhang, University of California, Berkeley and several disease resistance genes and additional control sequences provided by Roger Wise, Stacey Turner and Rico Caldo at Iowa State University and by Andris Kleinhofs.
Further Comments on the Assembly Used for the Barley1 Chip
As shown in the diagram below, the content of the Affymetrix Barley1 GeneChip was directly derived from a subset of HarvEST:Barley Assembly #21. Only the unigenes from Assembly #21 that had "good 3' ends" were transmitted to Affymetrix as exemplars, and of these only about 90% reached the final subset that was used directly for chip content design. The final subset of exemplar sequences unigenes from Assembly #21 is referred to as "Assembly #25". Judging by the number of rice and Arabidopsis gene models in Assemblies #21 and #25, it appears that the Barley1 GeneChip represents about 2/3 of the genes represented by Assembly #21 unigenes. Assembly #25 was also provided to colleagues at Iowa State University to be used as a core element of BarleyBase. Both assemblies are maintained in the HarvEST:Barley database and are available to others directly from Wanamaker and Close upon written request.
Comments on the Annotations Used for the Barley1 Chip
The November 2002 annotations of Assembly #25 unigenes were used as the formal annotations of the Barley1 GeneChip. In many cases, superior annotation existed for other, related Assembly #21 unigenes at the time of chip design. Also, reference databases have continued to improve since November 2002. Given the importance of correct annotation of probesets for data interpretations, HarvEST:Barley provides a powerful annotation tool to help Barley1 users make the most meaningful interpretations of data. These functions are available through "Search the Barley Chip" from the HarvEST:Barley Main Menu, as illustrated below.
HarvEST Main Page
HarvEST:Barley software and this web site copyright (c) 2001-2008 Steve Wanamaker, Timothy Close and the University of California.