Dear Rosaceae colleagues,
I am forwarding a note from Dr. Susan Brown at Cornell about forming four
sub-committees
that was discussed in Rosaceae community meeting held at IFTA conference
in Hershey, PA.
> Team Members Needed for Planning:
> There are four general theme areas of research in the Rosaceae white
paper (indicated in bold text below) and we are forming four sub
committees for planning purposes. Anyone with an interest in one or
more of these topics, and a willingness to participate in some
pre-organization work for strategic planning are encouraged to contact
the scientific coordinator for each group at the Email addresses below.
Please do not reply to the list serve. We would appreciate a response by
March 10th. Identifying those in each core area interested in
participating in the discussion will facilitate future strategic
planning. The Committee is charged with figuring out how such strategic
planning will happen and how it will be structured. The entire Rosaceae
community will participate in the strategic planning, but this committee
sets the framework.
> Reducing the dependence on chemical pesticides by improving biological
resistance: Herb Aldwinckle at hsa1(a)cornell.edu.
> Reducing labor costs (Plant architecture): Susan Brown at skb3(a)cornell.edu.
> Improving fresh and processed fruit quality, storage and safety: Abhaya
Dandekar at amdandekar(a)ucdavis.edu.
Improving profitability of the Rosaceae fruit industry (abiotic stress
tolerance): Michael Wisniewski at mwisniew(a)afrs.ars.usda.gov.
Dear All
This is to remind you that, registrations for the above conference close on
15 February 2006.
Registrations can be done online by visiting www.rgc3.co.nz
<http://www.rgc3.co.nz/> . Please complete both sections of the
registration process.
If you are requiring accommodation this also needs to be reserved through us
by 15 February as after that date we need to release any unallocated rooms.
Please ensure that when you register you include all activities that you may
wish to partake in as numbers need to be confirmed prior to conference.
If you have submitted an abstract and have not registered then we remind you
that you need to do so.
For those who have already registered, we look forward to meeting you at
Conference.
Regards Sue Page
Encore Events
PO Box 12097, Ahuriri, Napier
B 06 833 7440
F 06 833 7447
M 027 669 1345
E sue(a)encore-events.net.nz
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.
Subscription
Visit our mailing list site at GDR to be added/removed to the mailing
list. http://www.mainlab.clemson.edu/gdr/MailingList.shtml
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
Goodday everyone
Please note the following deadlines:
REGISTRATION - early bird closes on 31 December 2005, New Zealand time. To
take advantage of the early bird rate you can register online www.rgc3.co.nz
and click on the registration tab where you will find all the options
available. If you register online then please ensure you complete both
sections.
ABSTRACTS - for those who have submitted abstract titles and have not yet
submitted their abstract these are due by 31 December 2005, New Zealand
time. The instructions on the submission of abstracts and format
requirements are also available on http://www.rgc3.co.nz Please do not
forget to select the most appropriate topic area and include with the
abstract.
We have received a good number of very interesting titles and are looking
forward to the meeting.
Best wishes for a Very Merry Christmas and a Great 2006.
Regards Sue Page
Encore Events Management Ltd
13a Charles St, Westshore
Napier, New Zealand
Ph/Fax (06) 835 9549
Mobile (027) 669 1345
Email encore.events(a)clear.net.nz
Dear All
Thank you to those who have already submitted Abstract Titles for the above
conference.
However, we wish to remind all those who haven't submitted anything yet that
the FINAL DAY FOR SUBMISSION IS 31 OCTOBER 2005.
If you have any queries please refer to www.rgc3.co.nz, or contact me
direct.
We look forward to receiving your Abstract Titles.
Regards Sue Page
Conference Manager
Encore Events Management Ltd
13a Charles Street
Napier, New Zealand
Ph/Fax: (06)835 9549
Mobile: 027 669 1345
Email: encore.events(a)clear.net.nz
Hello everyone,
In addition to the RGC3 conference in Napier, a pre-conference workshop will
be held in Auckland, 13-17 March 2006. The call for application this
workshop was originally 15 October 2005 but is now being extended to 15
November 2005.
Please pass the information to any graduate student / young researcher /
colleague who may be interested in attending this workshop.
A description of the workshop is available on the RCG3 website,
www.rgc3.co.nz.
Best regards David Chagne
Pre-conference Workshop organiser
Hello everyone
We are pleased to announce that the registration information is now
available on our website http://www.rgc3.co.nz Please pass this information
on to any colleagues who may be interested in attending this conference.
Please read all the information carefully before commencing the registration
process.
To register online - you will need to complete the online registration form,
submit this, then you will be taken to a secure site to process the payment
for the registration fee and any activities you select.
Alternatively you can download the registration form from the Registration
Page and either send in by mail or fax through.
If you have any queries please do not hesitate to contact us.
REMINDER - that abstract titles are due in by 31 October 2005.
As you will see from the website the programme and activites are exciting
and we are looking forward to an excellent conference and meeting you there.
Regards Sue Page
Conference Organiser
Encore Events Management Ltd
13a Charles Street
Napier, New Zealand
Ph/Fax: + 64 (06)835 9549
Mobile: + 64 027 669 1345
Email: encore.events(a)clear.net.nz
GDR Newsletter August 2005
Welcome to the third issue of the GDR newsletter. This newsletter is
issued quarterly 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/newsletter0705.shtml
Attached is the pdf version of this newsletter.
What's new at GDR?
1. GDR web address change
2. Updates to peach transcriptome map
3. Anchored genes and ESTs are displayed in genetic maps in CMap
4. New EST data
5. Run InterProScan directly from the EST detail page
6. Bulk search and download feature available in the EST search pages.
7. Abstracts and powerpoint presentations of NRI funded projects available
Community News
1. International Symposium on Biotechnology of Temperate Fruit Crops and
Tropical Species, Daytona Beach, FL USA, October 10-14, 2005
2. 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.
3. 3rd International Rosaceae Genomics Conference in Napier, New Zealand,
March 19-23, 2006
What's new at GDR?
1. GDR web address change.
GDR is now accessible at the following URL: http://www.rosaceae.org. At
the current time this URL will be redirected to
http://www.mainlab.clemson.edu/gdr while we move the database over to the
new web address. In all future web references to GDR please use the
http://www.rosaceae.org URL.
2. Updates to peach transcriptome map.
Unique peach ESTs are being hybridized to peach BACs to map the ESTs onto
the genetically anchored peach physical map. 569 peach unigenes are
anchored to various Rosaceae genetic maps. 367 of them are anchored by
direct hybridization to genetically anchored BACs and the rest (202) are
anchored by hybridization to BACs that belong to genetically anchored BAC
contigs. 375 unigenes are anchored to the TxE map. GDR map viewer and the
downloadable peach transcriptome data reflects the updated peach
transcriptome map.
3. Anchored genes and ESTs are displayed in genetic maps in CMap.
The 25 major genes affecting agronomic characters, anchored to TxE map
(Dirlewanger et al, 2004), are now displayed in TxE map in CMap.The peach
ESTs are also displayed by the markers with which they share BACs or BAC
contigs in hybridization in eight Prunus genetic maps. The anchored ESTs
and markers in CMap are linked to GDR detail pages. View an example CMap
page.
4. New EST data
A new peach EST dataset sequenced by Elisa Vendramin from the CRA Istituto
Sperimentale per la Frutticoltura is now publicly available. A total of
1667 clones from peach fruit mesocarp have been analyzed. Assembly of
these ESTs produced 1116 putative peach unigenes within this dataset.
5. Run protein motif and domain searches using InterProScan.
Users can now search ESTs against the European Bioinformatics Institutes
InterPro database directly from GDR. InterPro is a database of protein
families, domains and functional sites in which identifiable features
found in known proteins can be applied to translated ESTs. Finding
functional domains in a EST may corroborate the putative function obtained
by sequence homology or provide more information for ESTs with no homology
to other known proteins. Our site programmatically accesses EBI's
InterProScan so users can query InterPro without uploading EST sequences
at the EBI's site. To access an example EST page, go to
(http://www.mainlab.clemson.edu/java/gdr/EST.jsp?
CloneName_Result=PP_LEa0002H11f)
and run InterProScan.
6. Bulk search and download feature available in the EST search pages.
A bulk search is available for peach, almond, strawberry, and GenBank
rosaceae EST datasets. Users can upload a file with multiple clone names
or Genbank accession numbers and have returned to them all the sequence
and homology information
associated with those sequences. Any bulk EST search query will now return
downloadable files of fasta formatted sequence and homology results.
7. Abstracts and powerpoint presentations of NRI funded projects.
View and download all the abstracts and powerpoint presentations of the
NRI funded projects presented at the recent ASHS meeting. Many thanks to
the authors and Dr Ed Kaleiko for providing us with this information.
Subscription
Visit our mailing list site at GDR to be added/removed to the mailing
list. http://www.mainlab.clemson.edu/gdr/MailingList.shtml
Work in progress
Processing new peach shoot ESTs, rose ESTs from vegetative apices and
apices at floral transition and blackberry ESTs
Extending the gene and QTL data available in CMap.
Integrating data from the USDA CSREES NRI projects
Developing a rosaceae EST unigene v2 with enhanced annotation