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Re: [CottonGen] [ICGI] A survey about using cotton genome resources

by Andrew Paterson

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

12 years, 6 months

A survey about using cotton genome resources

by Yu, Jing

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

12 years, 6 months

The draft G. raimondii sequence data is now in CottonGen

by Yu, Jing

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

12 years, 11 months

Plant Breeding courses

by ALLEN VAN DEYNZE

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>.

13 years, 4 months

Apologies for the two empty emails you received from this list

by Main, Doreen

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/>

13 years, 6 months

(no subject)

by mohamed abdalla

Prof. Mohamed Mohamed Aly Abdalla Prof. of Horticulture Assiut University 71526 Assiut, Egypt. Cellular: +20 127433025 Office : +20 882412888

13 years, 6 months

(no subject)

by Lanka Venkata Sai Krishna

post the list

13 years, 6 months

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