Gramene News

Plant Biology 2012

kclark — Fri, 27 Jan 2012 16:35:48 +0000

Registration is now open for the Plant Biology 2012 meeting to be held August 22-24 in Austin, Texas.

Gramene database interim build 34b released

marcela — Wed, 11 Jan 2012 20:59:54 +0000

The Gramene team is happy to announce interim release 34b. We have now added the reference genome for Cyanidioschyzon merolae 10D, a primitive unicellular red alga, which lives in acidic hot water (like hot springs), bringing us to 23 genomes. We updated the software of our Ensembl genome browser to version 65, updated the gene models for Physcomitrella patens (moss), updated the gene and prediction tables for the Oryza glaberrima (African rice) and Glycine max (soybean) core databases, and updated the gene BioMarts. We also updated the Compara gene trees to exclude superfluous Fgenesh predictions of G. max and O. glaberrima, and added genes from the partial Oryza genomes (the chromosome 3 short arm projects of wild species of Oryza). To accommodate these, we developed an entirely distinct set of gene trees focused on the Oryza genus, which include 12 complete and partial genomes of cultivated and wild relatives, plus several outgroup species. Unfortunately we no longer provide direct access to the Pan Compara gene trees, but these can still be accessed from EnsemblPlants. We are also releasing to the community, lists of candidates for putative annotation artifacts resulted from Gramene’s screen for split gene models in gene trees, the data can be found on our ftp site. Please let us know if you have and problems or question with the new build.

2012 Maize Genetics Conference

kclark — Fri, 06 Jan 2012 17:26:36 +0000

The 54th Annual Maize Genetics Conference will be held at the Doubletree Hotel in Portland, Oregon, from March 15-18, 2012. This year’s meeting will feature four plenary speakers: Bill Tracy (Univ. of Wisconsin-Madison), Venkatesan Sundaresan (Univ. of California, Davis), Jenny Graves (Australian National University), and Thomas Dresselhaus (Univ. of Regensburg). Further details about the program, registration for meeting and housing, abstracts, and transportation are available at the meeting website. All registration deadlines are January 31, 2012.

Introduction to Bio-Ontologies, Feb. 5, 2012

kclark — Fri, 06 Jan 2012 17:23:42 +0000

On the morning of Sunday, February 5, 2012, the Plant Ontology Consortium will host a tutorial on bio-ontologies to take place at the New York Botanical Garden. Further details are available at bioontology.org.

Gramene at PAG XX

kclark — Thu, 05 Jan 2012 16:11:52 +0000

Gramene will be present at next week’s Plant and Animal Genome (PAG) XX meeting in San Diego, CA from January 14-18, 2012. On Tuesday, January 17, we will present a workshop from 3:50 PM-6:00 PM in the California Room. We will also participate in a Plant Genomics Outreach booth (#423) with other members of the plant community to answer your questions about furthering your research with our resources. Finally, we will be presenting the following posters:

P0856 Metabolic and Regulatory Networks for Cereals
P0858 MaizeCyc: Metabolic Networks in Maize
P0951 Gramene: A Resource for Phylogenomics Study of the Oryza Genus
P0952 Gramene Genetic Diversity Module: A Plant Genotype-Phenotype Association Data Repository
P0993 TASSEL 4.0: Faster, Larger Diversity Analysis: It’s All About the Bits

Assistant/Associate Professor of Plant Breeding Genetics (Tenure Track) at Cornell University

pankaj — Tue, 03 Jan 2012 17:24:16 +0000

Responsibilities: Advances in biochemistry, metabolomics, and metabolic engineering, and the availability of genomic sequences for food crop species are opening new and valuable research opportunities for plant breeding. This molecular breeding position will have responsibility for conducting innovative research exploring genetic/epigenetic/quantitative variation in plants and the association with phenotypic variation in traits relating to human and animal health and nutrition made accessible by the latest technologies. These efforts could be applied to traditional or specialty crops chosen specifically for their unique attributes. The range of possible outcomes would span foods with new nutritional and health-promoting functions or bioavailability, to the chemistry of flavors and texture to new bioactive food components. Because this is part of a cluster hire, preference will be given to candidates interested in forming collaborations with other faculty with complementary expertise in nutritional sciences, food science, and animal science, among others. Appointee will be expected to develop an externally funded research program; release novel lines, germplasm or genetic stocks; supervise graduate students; teach courses at both the undergraduate and graduate levels related to plant breeding, plant genetics and genomics; and contribute to specialized courses, seminars, and team-taught courses, as well as to graduate training in plant breeding/plant genetics/genomics/plant molecular biology. We are seeking highly motivated individuals with strong research and teaching credentials. Strength in quantitative genetics/statistics is highly desirable. This position will have a 60:40 research and teaching responsibility. For more information visit our web site http://plbrgen.cals.cornell.edu.

Qualifications:
• Ph.D. in plant breeding, plant genetics/genomics, or plant molecular biology
• Experience in teaching, student advising, and research related to this position, either post-doctoral or pre-doctoral
• Evidence of ability to work with other researchers in interdisciplinary inquiry
• Evidence of ability to attract extramural support and lead an innovative research/ breeding program
• Postdoctoral and/or other relevant experience desirable.

Salary: Competitive and commensurate with background and experience. An attractive fringe benefits package is available.

Applications: Candidates are requested to submit a letter of application; detailed resume; a personal statement of research and teaching experience, leadership efforts, and contribution to diversity; copies of university transcripts; copies of one or two publications; and names and contact information for three references combined into a single file in pdf format. Send by e-mail to Ms. Michelle Steigerwald (md464@cornell.edu) or by mail to Department of Plant Breeding and Genetics, 240 Emerson Hall, Cornell University, Ithaca, NY 14853. Reviews will start after (Feb 1, 2012). Inquiries may be sent to Mark Sorrells, 240 Emerson Hall, Cornell University, Ithaca, NY 14853-1901; mes12@cornell.edu; 607-255-2180; 607-255-6683 (fax).

Cornell University, located in Ithaca, New York, is an inclusive, dynamic, and innovative Ivy League university and New York’s land-grant institution. Its staff, faculty, and students impart an uncommon sense of larger purpose and contribute creative ideas and best practices to further the university’s mission of teaching, research, and outreach.

Cornell University is an affirmative action/equal opportunity employer and educator.

New version of Flapjack released

kclark — Tue, 13 Dec 2011 15:46:08 +0000

The developers of Flapjack have released a new version (1.11.12.13). Flapjack is a tool for visualizing genotypic and haplotype data that "can handle the large data volumes generated by high throughput SNP and comparable genotyping technologies." Gramene’s diversity data sets are available in Flapjack format. We encourage you to extend your analysis of our data using tools like Flapjack.

Pigeonpea Genome: First Draft Published

pankaj — Wed, 02 Nov 2011 16:40:28 +0000

The first draft of the pigeonpea (Cajanus cajan) geneome of the variety ‘Asha’ was published last week in two separate but similar reports. Singh et al. reported 10x coverage of the genome revealing 510.81 Mb of of the 833.07 Mb genome size and 47,004 protein coding genes. Another study published almost simultaneously by Varshney et al. in an International collaboration lead by the ICRISAT reported 72.7% (605.78 Mb) of the 833.07 Mb pigeonpea genome with 48,680 predicted protein coding genes. Both studies found number of disease resistance genes and an enriched set of genetic markers which will help the legume breeders in improving pigeonpea varieties.

Pigeonpea is an important grain legume of the South Asia (Indian subcontinent), South-East Asia and East Africa. According to the lead author Dr. NK Singh, this is the first plant genome sequencing project completed entirely through a network of Indian institutions supported by the Indian Council of Agricultural Research. Author Dr. RK Varshney reports that this is the first plant genome project lead by the CGIAR and the ICRISAT.

Gramene build 34 released

kclark — Wed, 19 Oct 2011 16:18:51 +0000

The Gramene team is happy to announce the 34th major release of the site. In our Ensembl genome browser, six genomes have been updated and we have added Glycine max (soybean), Selaginella moellendorffii, Chlamydomonas reinhardtii bringing us to 22 genomes. We have also updated the genome browser to Ensembl version 64, updated blastz-chain-net whole genome alignments for new and updated genomes, built new Compara gene trees, and updated protein domain annotaions, cross-references and gene ontology (GO) projections. The BioMart data mining tool has updated plant gene and variation databases. Our ontologies database has been updated to the latest releases of GO, plant ontology (PO), and trait ontology (TO) and includes many new associations to the genomes and genes of our new species. Our Pathways section now has official release versions of MaizeCyc and BrachyCyc, and non-plant pathways were removed from RiceCyc, SorghumCyc, and BrachyCyc. The diversity section contains a new rice study of 14 agronomic traits from 226K SNPs across 374 lines from Huang X, et al, Nat Genet 2010, the 3.06 version of NSF Arabidopsis 2010 Project 250K chip study, phenotype data from single-gene studies, and a new association viewer for Arabidopsis variation data which is also linked from our Arabidopsis Ensembl genome browser. Several Oryza germplasm have been added to our germplasm database to bring the total to 13,265 records with links to Gramene’s markers, map sets, genes and proteins, and our distributed annotation server (DAS) has been updated with the latest alignments for all our species. Please let us know if you have and problems or question with the new build.

BrachyCyc: A metabolic pathway network of Brachypodium genes

kclark — Thu, 13 Oct 2011 15:54:39 +0000

We are pleased to announce the release of the BrachyCyc database. Developed by the Gramene database project, BrachyCyc is a catalog of predicted metabolic pathways from Brachypodium distachyon. Pathways and genes presented in this catalog are primarily based on the annotations carried out by Gramene on the version 1.2 of the gene models and release 1.0 of the Brachypodium distachyon inbred line Bd21 genome. The database was created using the Pathway Tools PathoLogic module developed by Peter D. Karp and co-workers at the Bioinformatics Research Group at SRI International.

This is the first official version (2.0) released for BrachyCyc. Improvements to this version include removal of 26 non-plant pathways. The database will continue to undergo regular rounds of curation in order to integrate exciting new discoveries on biochemical pathways in Brachypodium. We welcome feedback from the research community to help us build a good quality network. You can reach us by sending a message to the BrachyCyc curators.