ITMI ESTs & Bioinformatics, Sept 2001

ITMI's coordination of ESTs & Bioinformatics is now being performed by a committee:
• Olin Anderson, Chair
• Philippe Leroy
• David Marshall
• Dave Matthews
• Wolfgang Michalek
• Kazuhiro Sato

Issues for ITMI coordination

• from Olin:
  • Getting everyone to share software, protocols, etc would help as always.
  • Unigene sets. How to do it, with what data? If 5 different sites come up with different lists of unique sequences to put on arrays, then how meaningful will comparisons be?
  • Are there any sites with long-term funding to store/distribute ESTs?
  • It would be good to get ITMI backing for releasing all mapped cDNA sequences.
• Mining ESTs for SSRs
• Mining EST assemblies from different varieties for SNPs
• Maintaining gene lists for microarrays
• Assigning/curating function to ESTs
• Cross relating wheat and barley ESTs and relating them to rice sequence
• Proposal
  • Spreadsheet templates for data submission? Something like Sample_map.xls? Would anybody use this?
  • Free-text contributions directly to GrainGenes via "Submit comment/correction"?

Triticeae EST sequencing projects


		In dbEST	Potential
Olin Anderson	USDA-ARS	57053	140,000
Andreas Graner	IPK	17707	150,000
Yasunari Ogihara	Yokohama City U	2130	100,000
Rod Wing	CUGI	49606	50,000
Robbie Waugh	SCRI		40,000
Keith Edwards	IACR Long Ashton		40,000
Michel Beckert	INRA Clermont-Ferrand		40,000
Mark Jordan	Agriculture and Agri-Food Canada		32,000
J.A. Singh	Agriculture and Agri-food Canada	1373
Sylvie Cloutier	Agriculture and Agri-Food Canada	1002
Kazuhiro Sato	Okayama U	428	30,000
Alan Schulman	U Helsinki		30,000
Peter Langridge	U Adelaide	988	25,000
R.G. Hermann	U Munich	1903
Philippe Joudrier	INRA, Montpellier	1562
Wolfgang Schuch	Zeneca	1510
Tim Holton	Southern Cross U	1152
Rudi Appels	CSIRO	1056
Jizeng Jia	Inst Crop Germplasm China	1052
Marilyn Warburton	CIMMYT	1038
M. Shariflou	U Sydney	1030
C. Feuillet	U Zurich	1008
Paul Bailey	JIC	972
Nicola Pecchioni	Istituto Sperimentale Cerealicoltura	957
Goplan Selvaraj	National Research Council Canada	762
Joseph M. Anderson	USDA-ARS	532

Existing Resources

• The Big Guns
  • TIGR Gene Indices for wheat and barley: www.tigr.org/tdb/tgi.shtml
    ESTs clustered into Tentative Consensi. Top 5 peptide hits. Assignment to plantwide Tentative Ortholog Groups ("TOGA"). Gene Ontology (GO) annotation. Alignment to rice BACs and Arabidopsis chromosomes ("Genome Views"). BLASTable target database.
  • NCBI UniGene sets for wheat and barley: www.ncbi.nlm.nih.gov/UniGene/
    ESTs clustered with gene sequences. Best BLASTX match against eight other species. Distribution vs. cDNA libraries. Freely downloadable.
  • Hot tip: Many of us have wished we could BLAST against a specific taxonomic group of sequences, e.g. Hordeum or Triticeae. This is easily done. At www.ncbi.nlm.nih.gov/blast/Blast.cgi?PAGE=Nucleotides, look for the box "Limit by entrez query" and enter "triticeae [orgn]".
• EST project sites with data
  • ITEC, wheat, barley, rye. 24000 total: http://wheat.pw.usda.gov/genome/
    
    • Downloadable FASTA files of processed sequences
    • BLASTable target datasets
    • Map locations. Clones that have been mapped are being painted green on the GrainGenes maps and linked to information about their best BLASTX hit.
  • US Wheat Genome Project, wheat, rye: http://wheat.pw.usda.gov/NSF/
    
    • Curated contig assembly for 51,000 wheat and 7,000 rye ESTs
    • Nucleotide sequence alignments for the contigs
    • All BLASTN and BLASTX hits for each EST and contig
    • Downloadable FASTA files of raw and processed sequences and contigs
    • Tracefiles viewable online individually, available in bulk on request
    • BLASTable target datasets
  • CUGI (Clemson), barley: www.genome.clemson.edu/projects/barley
    
    • Best SwissProt hits
    • Phred quality files
    • BLASTable target database
    • Downloadable FASTA files of processed sequences
  • IPK (Gatersleben), barley: http://hordeum.ipk-gatersleben.de/est/about.html
    Top ten BLASTX hits. Consensus sequences for clusters.
  • IACR (Long Ashton), wheat: www.cerealsdb.uk.net
    FASTA sequences and best BLASTN hit. BLASTable target database.
• Descriptions of other projects
  • Purdue, wheat: www.btny.purdue.edu/usda-ars/wheatgen/
  • CRC, Winnipeg, wheat: http://res2.agr.ca/winnipeg/biotech_gc.htm
  • Helsinki, barley: www.biocenter.helsinki.fi/bi/bare-1_html/est.htm
• Software
  • HarvEST, http://harvest.ucr.edu/
    Software and database for differential EST expression among libraries.
  • SQPR, http://wheat.pw.usda.gov/demos/SQPR/
    "Sequence Quality Plate Reader", GUI for processing sequencer traces through Phred.

Current activities and plans

• US Wheat Genome Project
  • Moving data to GrainGenes
  • Mapping 10,000 wheat ESTs against Chinese Spring deletion lines. So far 2500 tentatively mapped but only 100 confirmed.
  • These ESTs will also be screened against BAC libraries that are being used to assemble a D-genome physical map.
  • Attempting to assemble a Triticeae Unigene Set
  • Microarrays coming
• USDA-IFAFS Barley Genome Project
  • CUGI: "actively processing the EST sequences including development of unigene sets, clustering etc." Investigating reports of vector contamination in their barley EST sequences in GenBank. See also http://harvest.ucr.edu/barley.htm.
  • Roger Wise: Oligo arrays coming
• BBSRC project
  Barley and wheat microarrays coming from SCRI and IACR-Long Ashton
• INRA, Clermont-Ferrand
  ITEC ESTs: cleaning, clusterisation, assembly and automatic annotation (Gene Ontology approach)
• NCBI and TIGR
  In July GrainGenes visited NCBI (Lukas Wagner) and TIGR (John Quackenbush) to find out more about their existing and planned services for Triticeae.
  • About the idea of a "Triticeae Unigene Set":
    Both felt that pooling wheat and barley ESTs in their clustering procedures (NCBI's Unigenes, TIGR's Tentative Consensi) would give bad results. Their algorithms are designed to cluster sequences that are identical except for allelic variation, and split paralogs. Closely related orthologs such as rat/mouse would give some kind of intermediate unpredictable output so they don't do it. Instead they use a different algorithm for finding interspecies orthologs, NCBI's HomoloGene, TIGR's TOGA.
    We gave them the lecture on the A B and D genomes of wheat. Not something they'd ever dealt with before. They were relieved to know the genomes are available separately in diploids and let it go at that.
  • Both emphasized the importance of 3' sequences for proper clustering, whereas most of the Triticeae projects are focusing on 5'.
  • Both mentioned how valuable if would be if we were to mount a project for full-length cDNA sequencing. More useful in some ways than genome sequencing.
• NCBI
  Exporting maps from GrainGenes to their "Map Viewer". See examples for maize and rice, www.ncbi.nlm.nih.gov/cgi-bin/Entrez/map_search?chr=mays.inf&query=adh1 and www.ncbi.nlm.nih.gov/cgi-bin/Entrez/maps.cgi?ORG=rice

- Dave Matthews
Last updated 23 Sep 2001
Please send additions and corrections to matthews@greengenes.cit.cornell.edu.