Dear Colleagues,
We are pleased to inform you that Oxford Journals has published CottonGen's article in Nucleic Acids Research.
The open-access link to the online article is: http://nar.oxfordjournals.org/cgi/content/full/gkt1064?
ijkey=fcXHnQiFBc9po6s&keytype=ref
The full citation for the article is: Yu J, Jung S, Cheng CH, Ficklin SP, Lee T, Zheng P, Jones D, Percy R, Main D (2013) CottonGen: a genomics, genetics and breeding database for cotton research. Nucleic Acids Research 2013; doi: 10.1093/nar/gkt1064
Thank you for your support and contribution to CottonGen. We will continue to enhance CottonGen with new data and functionality to make it better serve the cotton community. As always we welcome your feedback and comments.
Best Regards,
The CottonGen Team
Greetings,
(This message is the same as one just distributed to ICGI members via the ICGI listserv, and so if you receive it as well as the CottonGen listserv, I apologize for the duplication.)
Please recognize approaching deadlines and upcoming events:
Nov. 1, 2013 PAG Discounted Registration rate deadline -- PAG Meeting (Jan.11-15)
Nov. 1 2013 PAG Poster Abstract Submission (submit through PAG website; presenters must register)
Nov. 8, 2013 PAG Deadline for 2014 PAG Cotton Workshop Abstract Submissions (invited speakers only; submit through PAG website)
Nov. 15, 2013 Discounted rate deadline for the "Cotton SNP Chip" (see information, see "News" at http://www.cottongen.org and previous email (copied below))
Dec. 13, 2013 Discounted Registration rate deadline -- Beltwide Cotton Conference ( Jan 6-8)-
Jan. 6-8, 2014 Beltwide Cotton Conference (New Orleans, Louisiana, USA Jan 6-8)-
Jan. 11-15, 2014 Plant and Aniimal Genome (PAG) Meeting (San Diego, California, USA, Jan.11-15)
Jan. 12, 4pm Cotton Genome Workshop, at PAG Meeting
Sept. 25, 2014 Biennial meeting of ICGI, Wuhan, Hubei, China (more information is forthcoming)
Best wishes,
David Stelly
Co-Chair, ICGI
COPY OF PREVIOUS EMAIL:
=============================================
A Cotton SNP Consortium is about to produce a Cotton SNP Chip with up to 70,000 public SNPs in the "Fixed Content" (on all Chips), including up to 50k intraspecific and 20k interspecific; up to 65k will involve the primary gene pool. In addition, up to 20,000 additional SNPs can be added to the sector known as "Add-on" content, which can vary from one batch of chips to another. The initial period for purchase is expected to end mid-November.
Please note that while most if not all of the multi-national participants in the Consortium are members of ICGI, neither the Consortium or Chip is ICGI-organized or sponsored.
If you are interested in obtaining additional information about the Chip, please contact me at the following EMAIL ADDRESS and SUBJECT LINE:
David M. Stelly <stelly(a)tamu.edu> SUBJECT LINE: "Cotton SNP Chip Information Request"
Some time after sending your email, you should receive an acknowledgment email in return.
Thanks,
David Stelly
Co-Chair
Dear CottonGen Members,
A Cotton SNP Consortium is about to produce a Cotton SNP Chip with up to 70,000 public SNPs in the "Fixed Content" (on all Chips), including up to 50k intraspecific and 20k interspecific; up to 65k will involve the primary gene pool. In addition, up to 20,000 additional SNPs can be added to the sector known as "Add-on" content, which can vary from one batch of chips to another. The initial period for purchase is expected to end mid-November.
Please note that while most if not all of the multi-national participants in the Consortium are members of ICGI, neither the Consortium or Chip is ICGI-organized or sponsored.
If you are interested in obtaining additional information about the Chip, please contact me at the following EMAIL ADDRESS and SUBJECT LINE:
David M. Stelly <stelly(a)tamu.edu> SUBJECT LINE: "Cotton SNP Chip Information Request"
Some time after sending your email, you should receive an acknowledgment email in return.
Thanks,
David Stelly
ICGI Co-Chair
Dear Cotton Community Members,
Please accept our apology for the email you received yesterday containing unsupported statements about a fellow member of CottonGen and ICGI. To rectify this situation we include below a clarification offered to us by Dr. Paterson. In the future, any communication requests from members to the CottonGen/ICGI mailing lists will be sent to the steering committees for approval before posting.
Sincerely,
Dorrie Main
CottonGen Principal Investigator
Note from Dr. Andrew Paterson in reply to Dr. Thea Wilkins second email regarding access to genomic resources.
Having noted yesterday the merit of Dr. Wilkins libraries, ICGI members also may wish to consider that non-profit distribution centers including Texas A&M, CUGI/AGI, and PGML have BACs from the same genotypes used by Dr WIlkins. While these BACs would lack the value added by Dr Wilkins sequencing, they may be much less costly to obtain than those from a private vendor.
Dr. Wilkins unsupported comments about my BAC distribution record are incorrect. My policies were formulated under an NSF grant on which Dr. Wilkins was the PI. These policies and my record have been regularly reviewed and found satisfactory by my research sponsors. We have had an online ordering system (http://www.plantgenome.uga.edu/catalog/index.php?cPath=1) for many years, and requests are filled promptly. All who have requested BACs from me have received them. Likewise, our probe sequences were deposited in Genbank soon after their completion, and genome sequences that I have overseen were publicly released nearly a year (for cotton, and nearly 2 years for sorghum) in advance of publication.
Best wishes to all.
Andrew Paterson, Chair, ICGI and
Regents Professor, University of Georgia.
Dorrie Main, Ph.D.
Associate Professor of Bioinformatics
Department of Horticulture
Washington State University
45 Johnson Hall
Pullman, WA 99164-6414
Tel: 509-335-2774
Email: dorrie(a)wsu.edu
URL: www.bioinfo.wsu.edu
Some may wish to be aware that there are other public BAC libraries available (on a cost-recovery basis) for the same genotypes, although they are not the specific libraries that were used in Thea's sequencing.
On Mar 26, 2013, at 1:05 PM, "Yu, Jing" <jing.yu(a)wsu.edu> wrote:
> Dear Cotton Researchers,
>
> Dr. Thea WIlkins would like to release all of her genome resources through Amplicon Express (for lists the type and cost of services, please visit http://ampliconexpress.com), as they maintain excellent QC and provide a range of services. However, she needs know if there is sufficient interest by the community for Amplicon to provide such services.
>
> The resources are 6 BAC libraries of excellent quality with >125 kb inserts as follows
> ~8X MboI G. Arboreum AKA8401 library anchored by Andy Paterson
> ~6X BamHI G. arboreum AKA 8401 library used to generate sequence-based physical map
> ~6X EcoRI G. arboreum AKA 8401 library used to generate sequence-based physical map
>> 5X Gossypiodes Kirkii BAC library generated for making sequence-based physical map
>> 5X G. Kirkii library generated for making a sequence-based physical map
> 5X G. hirsutum TM1 BAC library
>
> Please let us know if you are interested in using these resources via services provided by Amplicon Express within the next two weeks. If there is not enough interest, these important resources, which are not currently available to the community, will be lost to the community forever.
>
> Please reply to this email with either a “yes” or “no” (please use reply and not reply all).
>
> Thank you for your help.
>
> Dr. Jing Yu
> CottonGen Curator
> _______________________________________________
> Main Bioinformatics Laboratory
> ICGI-LIST mailing list
> ICGI-LIST(a)cottongen.org
>
>
>
________________
Andrew Paterson
Regents Professor and Head,
Plant Genome Mapping Laboratory (Dept #398)
University of Georgia
111 Riverbend Road, Rm 228
Athens GA 30605
(for UPS deliveries the zip code is 30605)
Phone 1-706-583-0162; Fax 1-706-583-0160; Email paterson(a)plantbio.uga.edu
Web site: http://www.plantgenome.uga.edu/
Program Coordinators:
Anne A. Ogden, 706-583-0166, ogden(a)uga.edu
Melissa D. Brock, 706-583-0161, mbrock(a)uga.edu
Dear Cotton Researchers,
Dr. Thea WIlkins would like to release all of her genome resources through Amplicon Express (for lists the type and cost of services, please visit http://ampliconexpress.com), as they maintain excellent QC and provide a range of services. However, she needs know if there is sufficient interest by the community for Amplicon to provide such services.
The resources are 6 BAC libraries of excellent quality with >125 kb inserts as follows
~8X MboI G. Arboreum AKA8401 library anchored by Andy Paterson
~6X BamHI G. arboreum AKA 8401 library used to generate sequence-based physical map
~6X EcoRI G. arboreum AKA 8401 library used to generate sequence-based physical map
>5X Gossypiodes Kirkii BAC library generated for making sequence-based physical map
>5X G. Kirkii library generated for making a sequence-based physical map
5X G. hirsutum TM1 BAC library
Please let us know if you are interested in using these resources via services provided by Amplicon Express within the next two weeks. If there is not enough interest, these important resources, which are not currently available to the community, will be lost to the community forever.
Please reply to this email with either a “yes” or “no” (please use reply and not reply all).
Thank you for your help.
Dr. Jing Yu
CottonGen Curator
Dear Cotton Researchers,
The CottonGen team is pleased to announce the availability of the draft G. raimondii (D genome) presented in the Wang et al., 2012 Nature Genetics publication, graciously provided by Drs. Shuxun Yu, Jun Wang and Yu-Xian Zhu to CottonGen. The assembly includes their pseudomolecules, predicted genes, non-coding RNA and repeats. In addition, the CottonGen team has aligned to the genome several commonly used resources such as CottonGen RFLP, SSR, and SNP markers, NCBI cotton dbSNP, CottonGen unigenes, PlantGDB unigenes, Josh Udall's 454-derived transcript contigs, NCBI cotton dbEST, NCBI cotton mRNA and protein sequences from various plant genomes. Additionally, the gene models have been annotated with Gene Ontology (GO), InterPro (IPR) domains and KEGG pathways and orthologs. The assembly and all ancillary annotations and alignments are available for exploration with GBrowse on the CottonGen website and are available for sequence comparison on our BLAST servers. All files are available for download on the CottonGen G. raimondii genome page or from our FTP repository.
In the near future we will be adding a page for each gene providing all functional and structural details. Another announcement will be sent when these additional resources are available.
Here are some quick links:
Draft G. raimondii genome page
http://www.cottongen.org/species/Gossypium_raimondii/bgi-cgp_genome_v1.0
GBrowse Viewer:
http://www.cottongen.org/gb/gbrowse/CGP_Dgenome/
FTP downloads:
ftp://ftp.bioinfo.wsu.edu/species/Gossypium_raimondii/CGP-BGI_G.raimondii_D…
NCBI BLAST (returns results to screen):
http://www.cottongen.org/tools/blast
Batch BLAST (returns results parsed in an excel file):
http://www.cottongen.org/tools/batch_blast
The CottonGen team
Dear ICGI member,
we would like to make you aware of upcoming courses in Plant Breeding developed by UC Davis, Asia Plant Breeding Academy and UC Davis Plant Breeding Academysm
Allen Van Deynze
UC Davis receives a royal visit from Thailand
Her Royal Highness Princess Maha Chakri Sirindhorn of Thailand visited UC Davis on May 14- 15, 2012. The Princess of Thailand and senior Thai academic scientists accompanying her showed high interest in the newest developments in agricultural and nutritional research presented to them by UC Davis faculty. HRH the Princess is a knowledgeable and dedicated patron of several charitable organizations that are active in agriculture, nutrition and community development in Thailand and other countries of Southeast Asia.
At the UC Davis workshop, Allen Van Deynze and Kent Branford of the UC Davis Seed Biotechnology Center (SBC) had the honor to present a summary of recent SBC activities. Allen described a new SBC educational program, the Asian Plant Breeding Academy that will begin in November 2012 in Thailand in collaboration with the Asian & Pacific Seed Association. Kent Bradford updated HRH the Princess on a novel technology (desiccant drying beads) that is being implemented to address the challenge of safely drying and storing seeds under humid conditions. This project, supported by a USAID-funded HortCRSP grant, is based on technology developed by a Thai company (Rhino Research Group, Phitchit) and is being implemented in Thailand, Nepal, Bangladesh, India, Kenya and other countries. Such expertise and methods will be instrumental for adoption of advanced seed technologies in Thailand's agricultural industry.
The UC Davis Plant Breeding Academy also begin in September, 2012 at UC Davis. For more information on the UC Davis, SBC and Plant Breeding Academy in Asia visit http://pba.ucdavis.edu or contact Jeannette Martins, jmartins(a)ucdavis.edu<mailto:jmartins@ucdavis.edu>.
Dear CottonGen Members,
Please accept our apologies for the two emails you have received from the CottonGen mailing list by members with no content included. We have changed the settings so that any postings go first to our curator for moderation. From now on you will only receive email communication from this list that we decide is pertinent to our members. As members you can still post to this list (cottongen-list(a)cottongen.org<mailto:cottongen-list@cottongen.org>) but it will be accepted or rejected by a moderator.
Sincerely
The CottonGen Development Team
Dorrie Main, PhD
Associate Professor of Bioinformatics
Dept. of Horticulture and landscape Architecture
Washington State University
45 Johnson Hall
Pullman, WA 99164-6414
Tel: 509-335-2774 (office)
Email: dorrie(a)wsu.edu<mailto:dorrie@wsu.edu><mailto:dorrie@wsu.edu>
URL: www.bioinfo.wsu.edu<http://www.bioinfo.wsu.edu/>
