Community Members:
Many of you have already voted for new members to RosEXEC. Be aware that
voting will terminate on 19 Nov, two weeks from now.
Please visit the GDR web site to cast your ballot electronically.
http://www.rosaceae.org/bio/content?title=&url=/cgi-bin/gdr/gdr_rosexec_memb
ership_2011_vote_form.cgi&style=height:1600px;width:950px
All community members are eligible to vote. Thanks! Jim
#####
James R. McFerson, PhD
WA Tree Fruit Research Commission & Vice-Chair, RosEXEC
1719 Springwater St
Wenatchee, WA 98801
work: 509.665.8271 x1
mob: 509.669.3900
Rosaceae Community Member:
We are ready to vote on the 2011 candidates for RosEXEC.
Voting begins 26 Oct and ends 19 Nov.
Please go to the following web site to learn about the candidates¹
background and vision for RosEXEC. Then submit your electronic ballot.
http://www.rosaceae.org/bio/content?title=&url=/cgi-bin/gdr/gdr_rosexec_memb
ership_2011_vote_form.cgi&style=height:1600px;width:940px
The community will elect five new U.S. members and two new International
members to a 3-year term. U.S.-based members will vote for both U.S.
candidates and International candidates. International community members
will vote for International candidates only.
This year¹s slate is diverse. We encourage you to consider voting to create
a leadership group that will appropriately represent the amazing diversity
of the Rosaceae community. Current RosEXEC membership can be found at
[http://www.rosaceae.org/node/291]
As a reminder, the mission of RosEXEC is to:
· 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.
Thanks again to the following U.S. and International members rotating off:
U.S. International
Chris Dardick David Chagné
Amit Dhingra Jasper Rees
Jim Luby Eric van de Weg
Cameron Peace
Gayle Volk
QUESTIONS?
Please contact Jim McFerson (mcferson(a)treefruitresearch.com), Chair, RosEXEC
membership committee.
VOTE EARLY!
Hi Folks,
The deadline to register is 5 pm PDT Friday October 22.
Thanks
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/>
Hi Folks,
If you are planning on attending the SNP summit in South Africa on November 13 and 14, can you please register using the form on GDR. http://www.rosaceae.org/node/375
Thanks
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/>
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.
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/>
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/>
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/>
________________________________
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
