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328 discussions

by Jim McFerson

LAST DAY TO NOMINATE CANDIDATES FOR ROSEXEC!!! EXTENDED NOMINATION DEADLINE 15 Oct 2010 We are seeking nominations of individuals to serve for a three-year term on the U.S. Genomics, Genetics, and Breeding Executive Committee (RosEXEC). There are five open seats on the 15 member Committee and 2 open seats for international liaisons. While we do have six individuals nominated already, we would like to receive at least another six nominations. Please consider nominating a colleague you believe would contribute to supporting the mission of RosEXEC: · Serve as a communication and coordination focal point for the U.S. Rosaceae genomics, genetics and breeding community. · Define research priorities based on input from the industry and research community. · Facilitate scientific interaction and foster dynamic research teams. · Promote research priorities. · Coordinate educational efforts from the research community to the industry and the public. Nomination of candidates who have not previously served on the RosEXEC and representatives of industry are encouraged. Members who will continue to serve in 2010 include Angela Baldo, Jim Hancock, Jim McFerson, Bryon Sosinski, Philip Stewart, Nahla Bassil, John Clark, Kevin Folta, Ksenija Gasic, Amy Iezzoni and Jay Norelli, so no need to nominate them as they will already be serving. International liaison members rotating off this year include Jasper Rees (Africa), Eric van de Weg (Europe). Remaining members through 2012 are Herman Silva (South America) and David Chagne (Aus/NZ). Two new members are needed to serve two year terms and we are seeking at least one to be in Europe. Prior to nomination, the nominator is required to contact the nominee and confirm willingness to serve on RosEXEC. Committee members are expected to participate in quarterly telephone conference meetings and provide several hours of work in support of the RosEXEC mission. Send nominations to Jim McFerson (mcferson(a)treefruitresearch.com), Chair of the RosEXEC membership committee, by 15 Oct 2010. Nominees will then be contacted by the membership committee and asked to provide a brief bio and vision statement. The community-wide election will be managed by the Genome Database for the Rosaceae (GDR) and held via internet from 25 Oct-19 Nov 2010. The next meeting of RosEXEC will be on 16 Jan 2011 in conjunction with the PAG Conference, San Diego CA.

14 years, 5 months

apple genome sequence and annotation available on GDR

by Main, Doreen

The apple genome sequence and associated annotation are now available in GDR. Many thanks to Riccardo Velasco and his team for providing the data. While there are links in the text below, please go to the GDR home page (www.rosaceae.org) to access the data as the email links sometimes get re-routed incorrectly via the mail server at WSU. Apple Genome v1.0 General Information * From this site you can browse and download the whole genome sequence of the Velaso et al., 2010 published apple genome assembly v1.0; predicted gene transcripts, their locations and putative function based on homology to known genes. You can BLAST your sequences against the genome sequence, the predicted genes and associated transcripts. You can search and browse the chromosomes, predicted genes and markers in GBrowse and view the evidence for each prediction and feature. Important Details About This Assembly * Because of the heterozygous nature of the Malus x domestica genome, pseudomolecules corresponding to the chromosomes are not presented. To preserve haplotype information, this assembly consists of sets of assembled contigs organized into metacontigs (clusters) and anchored to the chromosomes using 1,643 genetic markers. There is no consensus sequence from assembled contigs. Please see the whole genome <http://www.rosaceae.org/projects/apple_genome#publication> publication in Nature Genetics for further details. * Chromosomes are labeled 'chr1' through 'chr17' for each of the 17 chromosomes respectively. Contigs from different haplotypes may align and overlap on the same chromosomal region. Metacontigs that could not be anchored have been arranged sequentially in a chromosome-like feature named 'unanchored', however, the order of metacontigs on this "chromosome" is arbitrary. * Visualization of the genome using GBrowse <http://www.rosaceae.org/gb/gbrowse/malus_x_domestica> orients the contigs within a chromosome, however, gene predictions, location of markers, tRNA and protein alignments were constructed and aligned using contig sequences. * 5' and 3' UTR regions are currently not available for gene models. Data and Tools * Apple Genome Sequence * View the Apple v1.0 genome assembly and annotations in GBrowse <http://www.rosaceae.org/gb/gbrowse/malus_x_domestica> * Download the Malus x domestica genome contigs <http://www.rosaceae.org/system/files/apple_genome/Malus_x_domestica.v1.0.co…> (fasta, 278 MB compressed) * Download the Malus x domestica chloroplast sequence <http://www.rosaceae.org/system/files/apple_genome/Malus_x_domestica.v1.0.ch…> (fasta, 50 KB compressed) * Download the Malus x domestica mitochondrial sequence <http://www.rosaceae.org/system/files/apple_genome/Malus_x_domestica.v1.0.mi…> (fasta, 126KB compressed) * Apple Genome Sequence Predicted Genes * Download the predicted consensus gene set CDS sequences <http://www.rosaceae.org/system/files/apple_genome/Malus_x_domestica.v1.0.co…> (fasta, 18 MB compressed) * Download the predicted consensus gene set peptides sequences <http://www.rosaceae.org/system/files/apple_genome/Malus_x_domestica.v1.0.co…> (fasta, 12 MB compressed) * Download other gene prediction CDS sequences <http://www.rosaceae.org/system/files/apple_genome/Malus_x_domestica.v1.0.ot…> (fasta, 78 MB compressed) * Download other gene prediction peptides sequences <http://www.rosaceae.org/system/files/apple_genome/Malus_x_domestica.v1.0.ot…> (fasta, 49 MB compressed) * Predicted Gene Function * Download the non-redundant, best-match predicted protein homologs <http://www.rosaceae.org/system/files/apple_homo/Malus_x_domestica.v1.0_gene…> (excel, 59 MB) * Download species/database specific protein homologs: * 71,657 apple gene peptides with Arabidopsis homologs <http://www.rosaceae.org/system/files/apple_homo/Malus_x_domestica.v1.0_gene…> (excel, 78 MB) * 71,245 apple gene peptides with Swiss-Prot homologs <http://www.rosaceae.org/system/files/apple_homo/Malus_x_domestica.v1.0_gene…> (excel, 54 MB) * 84,380 apple gene peptides with TrEMBL homologs <http://www.rosaceae.org/system/files/apple_homo/Malus_x_domestica.v1.0_gene…> (excel, 68 MB) * 73,479 apple gene peptides with Grape homologs <http://www.rosaceae.org/system/files/apple_homo/Malus_x_domestica.v1.0_gene…> (excel, 62 MB) * 78,017 apple gene peptides with Peach homologs <http://www.rosaceae.org/system/files/apple_homo/Malus_x_domestica.v1.0_gene…> (excel, 66 MB) * 79,527 apple gene peptides with Poplar homologs <http://www.rosaceae.org/system/files/apple_homo/Malus_x_domestica.v1.0_gene…> (excel, 69 MB) * BLAST your sequences * using the GDR NCBI BLAST Server <http://www.rosaceae.org/bio/content?title=&url=http://app.bioinfo.wsu.edu/b…;> - results returned to your screen * using the GDR BATCH BLAST Server <http://www.rosaceae.org/bio/content?title=&url=/cgi-bin/gdr/gdr_blast> - upload many sequences and have the results parsed out in an excel file * Markers * Download the apple markers with links to GBrowse & CMAP <http://www.rosaceae.org/system/files/apple_genome/Malus_x_domestica.v1.0.ma…> * Questions or Comments? * Contact us with questions/feedback/comments (select the apple genome in the dropdown box in the contact form <http://www.rosaceae.org/contact> ) * Whole Genome Publication * Riccardo Velasco , Andrey Zharkikh , Jason Affourtit , Amit Dhingra , Alessandro Cestaro , Ananth Kalyanaraman , Paolo Fontana , Satish K Bhatnagar , Michela Troggio , Dmitry Pruss , Silvio Salvi , Massimo Pindo , Paolo Baldi , Sara Castelletti , Marina Cavaiuolo , Giuseppina Coppola , Fabrizio Costa , Valentina Cova , Antonio Dal Ri , Vadim Goremykin , Matteo Komjanc , Sara Longhi , Pierluigi Magnago , Giulia Malacarne , Mickael Malnoy , Diego Micheletti , Marco Moretto , Michele Perazzolli , Azeddine Si-Ammour , Silvia Vezzulli , Elena Zini , Glenn Eldredge , Lisa M Fitzgerald , Natalia Gutin , Jerry Lanchbury , Teresita Macalma , Jeff T Mitchell , Julia Reid , Bryan Wardell , Chinnappa Kodira , Zhoutao Chen , Brian Desany , Faheem Niazi , Melinda Palmer , Tyson Koepke , Derick Jiwan begin_of_the_skype_highlighting end_of_the_skype_highlighting , Scott Schaeffer, Vandhana Krishnan , Changjun Wu , Vu T Chu , Stephen T King , Jessica Vick , Quanzhou Tao , Amy Mraz , Aimee Stormo , Keith Stormo , Robert Bogden , Davide Ederle , Alessandra Stella , Alberto Vecchietti , Martin M Kater , Simona Masiero , Pauline Lasserre , Yves Lespinasse , Andrew C Allan , Vincent Bus , David Chagné , Ross N Crowhurst , Andrew P Gleave , Enrico Lavezzo , Jeffrey A Fawcett , Sebastian Proost , Pierre Rouzé , Lieven Sterck , Stefano Toppo , Barbara Lazzari , Roger P Hellens , Charles-Eric Durel , Alexander Gutin , Roger E Bumgarner , Susan E Gardiner , Mark Skolnick , Michael Egholm , Yves Van de Peer , Francesco Salamini & Roberto Viola. The Genome of the Domesticated Apple (Malus x domestica Borkh.) <http://dev.rosaceae.org/bio/content/?title=&url=http://www.rosaceae.org/cgi…;> Nature Genetics 42, 833-839. 2010. Dorrie Main, PhD Associate Professor of Bioinformatics Dept of Horticulture and Landscape Architecture Washington State University 45 Johnson Hall, Pullman, WA 99164-6414 Email: dorrie(a)wsu.edu Tel: (509) 335 2774 Fax: (509) 335 8690 URL: www.bioinfo.wsu.edu <http://www.bioinfo.wsu.edu/>

14 years, 5 months

RosEXEC Nominations extended

by Main, Doreen

EXTENDED NOMINATION DEADLINE 15 Oct 2010 We are seeking nominations of individuals to serve for a three-year term on the U.S. Genomics, Genetics, and Breeding Executive Committee (RosEXEC). There are five open seats on the 15 member Committee and 2 open seats for international liaisons. While we do have six individuals nominated already, we would like to receive at least another six nominations. Please consider nominating a colleague you believe would contribute to supporting the mission of RosEXEC: * *****Serve as a communication and coordination focal point for the U.S. Rosaceae genomics, genetics and breeding community. * *****Define research priorities based on input from the industry and research community. * *****Facilitate scientific interaction and foster dynamic research teams. * *****Promote research priorities. * *****Coordinate educational efforts from the research community to the industry and the public. Nomination of candidates who have not previously served on the RosEXEC and representatives of industry are encouraged. Members who will continue to serve in 2010 include Angela Baldo, Jim Hancock, Jim McFerson, Bryon Sosinski, Philip Stewart, Nahla Bassil, John Clark, Kevin Folta, Ksenija Gasic, Amy Iezzoni and Jay Norelli, so no need to nominate them as they will already be serving. International liaison members rotating off this year include Jasper Rees (Africa), Eric van de Weg (Europe). Remaining members through 2012 are Herman Silva (South America) and David Chagne (Aus/NZ). Two new members are needed to serve two year terms and we are seeking at least one to be in Europe. Prior to nomination, the nominator is required to contact the nominee and confirm willingness to serve on RosEXEC. Committee members are expected to participate in quarterly telephone conference meetings and provide several hours of work in support of the RosEXEC mission. Send nominations to Jim McFerson (mcferson(a)treefruitresearch.com), Chair of the RosEXEC membership committee, by 15 Oct 2010. Nominees will then be contacted by the membership committee and asked to provide a brief bio and vision statement. The community-wide election will be managed by the Genome Database for the Rosaceae (GDR) and held via internet from 25 Oct-19 Nov 2010. The next meeting of RosEXEC will be on 16 Jan 2011 in conjunction with the PAG Conference, San Diego CA. Dorrie Main, PhD Associate Professor of Bioinformatics Dept of Horticulture and Landscape Architecture Washington State University 45 Johnson Hall, Pullman, WA 99164-6414 Email: dorrie(a)wsu.edu Tel: (509) 335 2774 Fax: (509) 335 8690 URL: www.bioinfo.wsu.edu <http://www.bioinfo.wsu.edu/>

14 years, 5 months

Italian-led international research consortium decodes the apple genome

by Main, Doreen

The apple genome was today published by the Italian-led international consortium. Please find attached their press release. Congratulations to all concerned for this important work. The GDR team have the genome data and we hope to release it very soon on GDR. We will send out another email when it is available on GDR. Dorrie Main, PhD Associate Professor of Bioinformatics Dept of Horticulture and Landscape Architecture Washington State University 45 Johnson Hall, Pullman, WA 99164-6414 Email: dorrie(a)wsu.edu Tel: (509) 335 2774 Fax: (509) 335 8690 URL: www.bioinfo.wsu.edu <http://www.bioinfo.wsu.edu/>

14 years, 6 months

RGC5 Oral Submissions due date next Monday

by Main, Doreen

________________________________ From: Jasper Rees [mailto:reesj@arc.agric.za] Sent: Fri 8/13/2010 3:23 AM To: Main, Doreen Subject: RGC5 Oral Submissions due date next Monday Hi Dorrie, can you post this on the gdr-list please? To remind people that we have a due date for oral abstracts for RGC5 that is coming up on Monday! Many thanks! j --- Dr D Jasper G Rees Tel +27 12 529 9101/9106 Head: Biotechnology Platform Cell +27 82 415 9295 Agricultural Research Council FAX +27 12 565 4667 Private Bag X05 Skype: jasperrees Onderstepoort, 0110 Email: ReesJ(a)arc.agric.za South Africa

14 years, 7 months

RCG5 student funding support enquiry

by Main, Doreen

Dear US Based Rosaceae Researchers, We would like to compile a list of potential student applicants who would like to attend RCG5 if they had some financial support. If you have any students who fit this category and would present a poster or talk, could you send us the following information about them so we can submit it to the NSF in support of our application for funding. NAME of STUDENT: GENDER: ETHNICITY: ORGANISATION: AREA of RESEARCH: SUPERVISOR NAME: Many Thanks Dorrie Main and Bryon Sosinski Dorrie Main, PhD Associate Professor of Bioinformatics Dept of Horticulture and Landscape Architecture Washington State University 45 Johnson Hall, Pullman, WA 99164-6414 Email: dorrie(a)wsu.edu Tel: (509) 335 2774 Fax: (509) 335 8690 URL: www.bioinfo.wsu.edu <http://www.bioinfo.wsu.edu/>

14 years, 7 months

Call for nominations to US RosEXEC

by Norelli, Jay

Call for nomination of new members to US Rosaceae Genomics, Genetics and Breeding Executive Committee (RosEXEC): The mission of the RosEXEC is to: · Serve as a communication and coordination focal point for the US Rosaceae genomics, genetics and breeding community. · Define research priorities based on input from the industry and research community. · Facilitate scientific interaction and foster dynamic research teams. · Promote research priorities. · Coordinate educational efforts from the research community to the industry and the public. After 3 years of excellent service the following US members (Chris Dardick, Amit Dhingra, Jim Luby, Cameron Peace and Gayle Volk) are rotating off the RosEXEC committee in January 2011. In 2010, five new RosEXEC members will be elected to a 3 year term to replace them in January 2011. All members of the Rosaceae community are invited to nominate candidates for election. Nomination of candidates who have not previously served on the RosEXEC and representatives of industry are encouraged. Members who will continue to serve in 2011 include Angela Baldo, Jim Hancock, Jim McFerson, Bryon Sosinski, Philip Stewart, Nahla Bassil, John Clark, Kevin Folta, Ksenija Gasic, Amy Iezzoni and Jay Norelli, so no need to nominate them as they will already be serving. International liaison members rotating off this year include Jasper Rees (Africa) and Eric van de Weg (Europe). Remaining members through 2012 are Herman Silva (South America) and David Chagné (Aus/NZ). Two new members are needed to serve two year terms where we are seeking at least one to be in Europe. Please nominate candidates to serve as international liaisons and confirm their interest before submitting your nominations, as described below. Prior to nomination, the nominator is required to contact the nominee and confirm their willingness to serve on RosEXEC. Committee members are expected to participate in quarterly telephone conference meetings and provide several hours of work in support of the RosEXEC mission. Nominations should be sent to Jim McFerson (mcferson(a)treefruitresearch.com <mailto:mcferson@treefruitresearch.com> ) Chair of the RosEXEC membership committee, and/or Jay Norelli (jay.norelli(a)ars.usda.gov <file:///C:\Documents%20and%20Settings\jnorelli\My%20Documents\Administration\Rosaceae%20Community\RosEXEC%20officer\July%208%20meeting\jay.norelli@ars.usda.gov> ) RosEXEC Secretary, by September 1, 2010. Nominees will then be contacted by the membership committee and asked to provide a CV or bio, and a brief vision statement. The community-wide election will be held in November.

14 years, 7 months

Rosaceae SNP Summit Information

by Main, Doreen

A Rosaceae community SNP Summit will be held at the Wallenberg Centre, Stellenbosch University in Stellenbosch, Cape Town, South Africa, on the 13th and 14th of November 2010. This will be immediately prior to the 5th International Rosaceae Genomics Conference to be held on the 14-17th of November 2010 at the same location. At the SNP Summit, hosted by the USDA NIFA funded RosBREED project (www.rosbreed.org <http://www.rosbreed.org/> ), RosBREED participants and other interested community members will decide on the best SNP genotyping platform to conduct genome scans within Rosaceae (apple, peach, cherry and strawberry) and select the sequences to be included on the platform. If you are interested in attending the SNP summit, please contact Dorrie Main (RosBREED Genomics Team Leader at dorrie(a)bioinfo.wsu.edu <mailto:dorrie@bioinfo.wsu.edu> . For more information on the RosBREED project, see www.rosbreed.org <http://www.rosbreed.org/> For more information on RGC5, see http://www.rgc5.co.za/ <http://www.rgc5.co.za/> Best Regards Dorrie Dorrie Main, PhD Associate Professor of Bioinformatics Dept of Horticulture and Landscape Architecture Washington State University 45 Johnson Hall, Pullman, WA 99164-6414 Email: dorrie(a)wsu.edu Tel: (509) 335 2774 Fax: (509) 335 8690 URL: www.bioinfo.wsu.edu <http://www.bioinfo.wsu.edu/>

14 years, 8 months

Announcing 5th International Rosaceae Genomics Conference in Cape Town SA, Nov 14-17, 2010

by Main, Doreen

RCG5 willl be held November 14-17, 2010 in Cape Town , South Africa. For full conference details, see the RCG5 website at http://www.rgc5.co.za <http://www.rgc5.co.za> Dorrie Main, PhD Associate Professor of Bioinformatics Dept of Horticulture and Landscape Architecture Washington State University 45 Johnson Hall, Pullman, WA 99164-6414 Email: dorrie(a)wsu.edu Tel: (509) 335 2774 Fax: (509) 335 8690 URL: www.bioinfo.wsu.edu <http://www.bioinfo.wsu.edu/>

14 years, 8 months

Peach Genome Release

by randalls＠bioinfo.wsu.edu

Hi Folks, Great news! The International Peach Genome Initiative (IPGA) has released version 1.0 of the peach genome sequence. Peach v1.0 currently consists of 8 pseudomolecules (the first 8 scaffolds) representing the 8 chromosomes of peach and are numbered according to their corresponding linkage groups (a total of 202 scaffolds were generated). The genome sequencing consisted of approximately 7.7 fold whole genome shotgun sequencing employing the accurate Sanger methodology, and was assembled using Arachne. The assembled peach scaffolds (total of 202) cover nearly 99% of the peach genome, with over 92% having confirmed orientation. To further validate the quality of the assembly, 74,757 Prunus ESTs were queried against the genome at 90% identity and 85% coverage, and we found that only ~2% were missing. This is truly a high quality genome! Gene prediction and annotation, is an ongoing process that may take years to complete, but current estimates indicate that peach has 28,689 transcripts and 27,852 genes. Peach v1.0 was generated from DNA from the doubled haploid cultivar 'Lovell' which means that the genes and intervening DNA is "fixed" or identical for all alleles and both chromosomal copies of the genome. This doubled haploid nature was confirmed by the evaluation of >200 SSRs, and has facilitated a highly accurate and consistent and assembly of the peach genome. For more information about the project and access to the peach genome data and tools go GDR(www.rosaceae.org/peach/genome/ <https://mail.cahnrs.wsu.edu/exchweb/bin/redir.asp?URL=http://www.rosaceae.o…> ), JGI (www.phytozome.org/peach/ <https://mail.cahnrs.wsu.edu/exchweb/bin/redir.asp?URL=http://www.phytozome.…> ) or the Istituto di Genomica Applicata (http://services.appliedgenomics.org/gbrowse/prunus_public/ <https://mail.cahnrs.wsu.edu/exchweb/bin/redir.asp?URL=http://services.appli…> ) Cheers The IPGA folks p.s. please note that GDR is now located at www.rosaceae.org <https://mail.cahnrs.wsu.edu/exchweb/bin/redir.asp?URL=https://mail.cahnrs.w…> , you will be redirected from the old GDR site to the new one. We will be sending out a newsletter about GDR very soon. Dorrie Main, PhD Associate Professor of Bioinformatics Dept of Horticulture and Landscape Architecture Washington State University 45 Johnson Hall, Pullman, WA 99164-6414 Email: dorrie(a)wsu.edu Tel: (509) 335 2774 Fax: (509) 335 8690 URL: www.bioinfo.wsu.edu <http://www.bioinfo.wsu.edu/> Randall Svancara Systems Administrator/DBA/Developer Main Bioinformatics Laboratory Randall Svancara Systems Administrator/DBA/Developer Main Bioinformatics Laboratory

14 years, 11 months

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