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GDR Newsletter January 2006 pdf attachment

by Sook Jung

19 years, 11 months

GDR Newsletter January 2006

by Sook Jung

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

19 years, 11 months

3rd International Rosaceae Genomics Conference - REMINDERS

by Neill & Sue Page

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

20 years

3rd International Rosaceae Genomics Conference - Abstract Titles

by Neill & Sue Page

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

20 years, 1 month

3rd International Rosaceae Genomics Conference - Pre-Conference Workshop

by Neill & Sue Page

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

20 years, 2 months

3rd International Rosaceae Genomics Conference - March 2006

by Neill & Sue Page

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

20 years, 2 months

GDR newsletter August 2005

by Sook Jung

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

20 years, 3 months

3rd International Rosaceae Genomics Conference

by Neill & Sue Page

Dear All We wish to advise that the website for the above conference, www.rgc3.co.nz, has now been updated to include the latest programme and Call for Papers. Please visit the site and complete the pre-registration form if you have not already done so. We will keep you informed as new information is loaded onto the website. If you have any queries please do not hesitate to contact me. Regards Sue Page Conference Organiser 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

20 years, 5 months

GDR newsletter April 2005

by Sook Jung

GDR Newsletter April 2005 Welcome to the second 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/newsletter0405.shtml Attached is the pdf version of this newsletter. Community News 1. View the projects funded through the 2004 USDA CSREES National Research Initiative. 2. Announcing 3rd International Rosaceae Genomics Conference in Napier, New Zealand, March 19-23, 2006 3. Rosaceae workshop to be held at the ASHS Annual Meeting in Las Vegas, NV, July 18-21, 2005 4. Download the notes from the 2005 Fruit and Nut Workshop at the Plant and Animal Genome Conference What's new at GDR? 1. Updates to peach physical map 2. Updates to CMap 3. Updates to Genbank Rosaceae EST data 4. Advanced EST search page available 5. Download/view transcriptome data 6. New feature in EST data page 7. Community page available 8. New online analysis tool, SSR server, is available 9. GDR Message Board available 10. GDR web address is changed 1. Updates to the peach physical map The latest peach physical map contains 16895 BACs 1388 contigs. A total of 152 contigs are anchored to the TxE map, the Prunus reference map. The current physical map data was generated from an FPC assembly done on January 6, 2004. WebFPC/WebChrom displays the peach physical map. 2. Updates to CMap 19 Rosaceae genetic maps are available through CMap, the comparative map viewer. Recent addition includes seven apple maps and two cherry maps archived from RoseDB by Anjela Baldo at USDA, ARS PGRU and peach PMP2 map. 3. Updates to GenBank Rosaceae EST data GenBank Rosaceae EST data have been annotated by sequence homology analyses against SwissProt database in addition to GenBank nr protein database. 4. Advanced EST search page available A new comprehensive EST search page is available for the EST datasets. Users can search ESTs in any combination of clone name, organism (genus, species), tissue type, putative function or species of the homologs, and anchored map position where relevant. The search results site has an option for downloading the sequences in fasta format. 5. Download/view transcriptome data The peach transcriptome page provides the current status of the peach transcriptome map and links to an Excel spreadsheet with transcriptome map data detail and other relevant resources. 6. New feature in EST data page A new option, "Printable Data" is available in the EST data page to present all the EST data in one page. View an example page. 7. Community page available Visit our community page for conference news, information on our outreach program and other community resources such as a list of the thirteen projects funded through the 2004 USDA CSREES National Research Initiative: Plant Genome, Bioinformatics, and Genetic Resources. 8. New online analysis tool, SSR server, is available GDR has implemented a new analysis tool, the SSR server. Using this online tool users can upload a batch file of sequences and have summary, individual and fasta formatted library file of the SSR containing sequences returned. The SSR server joins the growing list of online GDR tools such as the CAP3 assembly, FASTA and BLAST servers. 9. Searchable archives of GDR Message Board available Users can view the searchable archives from the gdr mailing list. If you are a registered gdr user you can use the GDR email mailing list gdr-list(a)genome.clemson.edu to send out community based information or requests from your own computer. These emails will automatically be archived onto the message board where they can be searched by subject, thread, author or date. 10. GDR web address is changed. GDR web address is now http://www.mainlab.clemson.edu/gdr/. The old address will be automatically redirected to the new address. Subscription Visit our mailing list site at GDR to be added/removed to the mailing list. http://www.genome.clemson.edu/gdr/MailingList.shtml Work in progress 1. Processing new peach shoot ESTs and rose ESTs from vegetative apices and apices at floral transition 2. EST search by uploading a list of clone names/accession numbers 3. EST search results site with bulk download feature: Excel files with sequence homology data for the EST search result sets can be downloaded. 4. Development of an online sequence processing tool where users can upload their sequence files (trace or seq and qual files) and have the high quality sequences returned. These in turn can be assembled using the existing CAP3 assembly tool, mined for SSRs using the SSR server and then searched against known plant proteins or rosaceae ESTs using the FASTA and BLAST servers. 5. Tutorials for search and analysis tools 6. Addition of more mapping data.

20 years, 7 months

3rd International Rosaceae Geonomis Conference

by Neill & Sue Page

Dear All Please find attached the First Announcement for the 3rd International Rosaceae Geonomics Conference which is being held in Napier, New Zealand 19-22 March 2006. Please feel free to forward/distribute this announcement to anyone that you feel may be interested in attending this conference. The website www.rgc3.co.nz is operational and you can complete the pre-registration form online or print out the attached and fax back or send by mail. If you have any queries please do not hesitate to contact me. Regards Sue Page Conference Organiser 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

20 years, 8 months

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