GDR Newsletter January 2006 - GDR-LIST

13 Jan 2006


      GDR Newsletter January 2006
Welcome to the fourth issue of the GDR newsletter. This newsletter is to
inform users about new or updated data and features in GDR and community
related news. Please feel free to provide feedback and news either
directly by email or via our online form. The online version can be found
at
http://www.mainlab.clemson.edu/gdr/newsletter/newsletter0106.shtml
Attached is the pdf version of this newsletter.
Community News
1. Fruit and Nut Workshop, Saturday January 14, 8 am-12 pm. Plant and
Animal Genome Conference XIV, San Diego, January 14-18, 2006. Conference
organizer: Dr Amy Iezzoni. A Rosaceae genomics roundtable meeting will be
held on Sunday January 15th, 8-10 am and the Rosaceae executive committee
will meet on Sunday January 15th, 10am-12pm.
2. 3rd International Rosaceae Genomics Conference will be held in Napier,
New Zealand, March 19-23, 2006.
3. The International Fruit Tree Association Annual Conference will be held
in Hershey, Pennsylvania, USA, February 26-March 1, 2006
What's new at GDR?
1. Proposal to renew funding for GDR submitted to the NSF Plant Genome
Program.
2. New EST libraries are available.
3. Rosaceae Unigene v2 with enhanced annotation available.
4. Prunus bin map data is available in CMap and marker search engine.
5. Enhanced SSR server now available with primer generating option.
6. More databases are available for blast/fasta sequence similarity search.
7. Data available for the three peach BACs that are completely sequenced.
8. New Roseaceae Genomics Executive Committee web page.
9. The GDR publications database now contains 242 papers relevant to
Rosaceae genetics/genomics.
1. GDR Renewal Proposal Submitted to NSF Plant Genome Program
In November 2005, a multi-institution proposal was submitted to the
National Science Foundation Plant Genome Program to renew funding support
for GDR through August 2009. The proposal if funded will significantly
enhance the functionality and usefulness of GDR for the rosaceae
community. If you's like more information on this proposal please contact
Dorrie Main.
2. New EST libraries are available.
The diploid strawberry species, Fragaria vesca, a putative genome donor to
the octoploid, cultivated species (Fragaria x ananassa) is being been
developed as a model system for genetic and genomic research in
strawberry.Tom Davis at the University of New Hampshire, USA, has provided
2717 ESTs from the unopened flower buds of diploid strawberries. A full
analysis results of his library can be viewed/downloaded from the project
page and the ESTs can be queried at the EST search site.
Peach (Prunus persica) represents a model species for prunus and a
reference species for Rosaceae. To develop an extensive Prunus EST
database for identification and cloning of genes important to fruit and
tree development, Bert Abbott at Clemson University, USA, generated 8832
high-quality expressed sequence tags (ESTs) from a peach cDNA library of
shoot tissue. After assembly and annotation, a putative peach unigene set
consisting of 5381 ESTs was defined. Full analysis results of his library
can be viewed/downloaded from the project page and the ESTs can be queried
at the EST search site.
3. Rosaceae Unigene v2 with enhanced annotation available.
A second version of the Rosaceae family unigene is now available. A new
assembly process is being utilized; the ESTs are assembled using CAP3
within each genera (Fragaria, Malus, Prunus, Pyrus, and Rosa), and these
assemblies are compiled and re-assembled together to produce the
family-wide unigene. The new Rosaceae Unigene contains 72114 unigenes.
Putative function has been assigned using the arabidopsis protein database
and will be further expanded using the swissprot and NCBI nr protein
databases. The unigenes have been analyzed for microsatellites and the
results including suggested primers can be downloaded. Please see each
project page (Fragaria, Malus, Prunus, Rosa and Rosaceae) to view/download
all the GDR unigene data.
4. Prunus bin map is available in CMap and marker search engine.
A Prunus bin map (Howad et al., 2005), is now available in GDR. CMap
displays the prunus bin map with bin names and the first/ last markers of
each bin, and the bin-mappded markers are displayed in each bin page. For
example, all the bin mapped markers of the first bin in G1 are shown in
bin 1:14 page. All the markers in the prunus bin map can be queried
through the GDR marker search page.
5. Enhanced SSR server now available with primer generating option.
The online SSR server at GDR has been enhanced to include an option to
have primers generated for the sequences that users wish to data mine for
microsatellites.
6. More databases are available for blast/fasta sequence similarity search.
The databases available for blast/fasta sequence similarity search
includes the following: peach ESTs, unigenes and ESTs with SSR's, BAC
anchored peach ESTs, mapped peach ESTs, almond ESTs and unigenes (Abbott,
Clemson U); peach ESTs and unigenes, peach ESTs with SSR's (Vendramin, CRA
ISF); octoploid strawberry ESTs, unigenes, and ESTs with SSRs (Folta, U of
Florida); diploid strawberry ESTs and unigenes (Davis, U of New
Hampshire); ESTs of Fragaria, Malus, Prunus, Pyrus, Rosa, and entire
Rosaceae family from NCBI dbEST; NCBI Rosaceae genomic sequences; NCBI
Rosaceae protein sequences; Arabidopsis protein sequences from TAIR. A
detailed description of the databases is available in each search engine.
The blast/fasta sequence servers return the output of the searches in both
parsed excel file and as a raw output file with visual alignments.
7. Data available for the three peach BACs that are completely sequenced.
Anchored ESTs/markers and the sequences for the three BACs (082I18, 028F08
and pPn31C7) can be accessed from BAC search site. An online annotation
pipeline is currently under development by the GDR team.
8. New Rosaceae Executive Committee web page created to provide a
communication portal for information and reports generated by the
committee.
9. The GDR publications database now contains 242 papers relevant to
Rosaceae genetics/genomics. New publications since our last newsletter are
listed below:
1. Lazzari B et al. ESTree db: a tool for peach functional genomics.
BMC Bioinformatics. 2005 Dec 1;6 Suppl 4:S16.
   2. Patocchi A, Walser M, Tartarini S, Broggini GA, Gennari F, Sansavini
S, Gessler C Identification by genome scanning approach (GSA) of a
microsatellite tightly associated with the apple scab resistance gene
Vm. Genome 2005 Aug;48(4):630-6.
   3. Oosumi T, Gruszewski HA, Blischak LA, Baxter AJ, Wadl PA, Shuman JL,
Veilleux RE, Shulaev V High-efficiency transformation of the diploid
strawberry (Fragaria vesca) for functional genomics. Planta. 2005 Dec
1;:1-12.
   4. Gillen, A.M., Bliss, F.A. Identification and Mapping of Markers
Linked to the Mi Gene for Root-knot Nematode Resistance in Peach J.
Amer. Soc. Hort. Sci. 130(1):24-33.
   5. Tzanetakis IE, Martin RR New features in the genus Ilarvirus
revealed by the nucleotide sequence of Fragaria chiloensis latent
virus. Virus Res 2005 Sep;112(1-2):32-7.
   6. Verde I, Lauria M, Dettori MT, Vendramin E, Balconi C, Micali S,
Wang Y, Marrazzo MT, Cipriani G, Hartings H, Testolin R, Abbott AG,
Motto M, Quarta R Microsatellite and AFLP markers in the Prunus persica
[L. (Batsch)]xP. ferganensis BC(1)linkage map: saturation and coverage
improvement. Theor Appl Genet 2005 Aug 9;:1-9.
   7. Howad W, Yamamoto T, Dirlewanger E, Testolin R, Cosson P, Cipriani
G, Monforte AJ, Georgi L, Abbott AG, Arus P Mapping with a Few Plants:
Using Selective Mapping for Microsatellite Saturation of the Prunus
Reference Map. Genetics 2005 Aug 22;.
   8. Holland D, Larkov O, Bar-Ya'akov I, Bar E, Zax A, Brandeis E, Ravid
U, Lewinsohn E Developmental and varietal differences in volatile ester
formation and acetyl-CoA: alcohol acetyl transferase activities in
apple (Malus domestica Borkh.) fruit. J Agric Food Chem 2005 Sep
7;53(18):7198-203.
   9. Gao ZS, Weg WE, Schaart JG, Arkel GV, Breiteneder H,
Hoffmann-Sommergruber K, Gilissen LJ Genomic characterization and
linkage mapping of the apple allergen genes Mal d 2 (thaumatin-like
protein) and Mal d 4 (profilin). Theor Appl Genet 2005 Sep 6;:1-11.
  10. Mohapatra A, Rout GR Identification and analysis of genetic
variation among rose cultivars using random amplified polymorphic DNA. Z
Naturforsch [C] 2005 Jul-Aug;60(7-8):611-7.
  11. Lalli DA, Decroocq V, Blenda AV, Schurdi-Levraud V, Garay L, Le Gall
O, Damsteegt V, Reighard GL, Abbott AG Identification and mapping of
resistance gene analogs (RGAs) in Prunus: a resistance map for Prunus.
Theor Appl Genet 2005 Sep 30;:1-10.
  12. Mehli L, Kjellsen TD, Dewey FM, Hietala AM A case study from the
interaction of strawberry and Botrytis cinerea highlights the benefits
of comonitoring both partners at genomic and mRNA level. New Phytol 2005
Nov;168(2):465-74.
  13. Lin C, Mueller LA, Carthy JM, Crouzillat D, Petiard V, Tanksley SD
Coffee and tomato share common gene repertoires as revealed by deep
sequencing of seed and cherry transcripts. Theor Appl Genet 2005 Nov
5;:1-17.
  14. Xie H, Sui Y, Chang FQ, Xu Y, Ma RC SSR allelic variation in almond
(Prunus dulcis Mill.). Theor Appl Genet 2005 Nov 24;:1-7.
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Work in progress
	Online EST sequence processing pipeline
	Annotating peach, plum and apricot BACs.
	Annotating the rosaceae unigene.
	Developing a rosaceae BAC annotation pipeline
	Extending the gene and QTL data available in CMap
	Integrating data from the USDA CSREES NRI projects