Gramene Workshop at the 2018 Maize Genetics Meeting in Saint-Malo, France

Have you ever needed to know if the maize gene you work on has an ortholog in sorghum or Arabidopsis?

Has the gene family that you are working on expanded or contracted relative to other crop or model grass species?

Is the biochemical pathway you work on conserved in sorghum and soybean? 

If so, you may want to explore these questions in the Gramene database!

In the context of the 2018 Maize Genetics Conference, Dr. Marcela Karey Tello-Ruiz will give an overview of the Gramene project during the pre-conference workshops on Thursday, March 22nd, 2018 at 2:30 PM in the Charcot Room of the Palais du Grand Large at Saint-Malo, France.

Click here for the workshop SLIDES and some EXERCISES.

Mining Maize with Gramene...

Gramene is an integrated resource for comparative functional analysis in plants. Gramene provides researchers with access to 53 genomes, and pathways for 75 plant species, including Zea mays B73 (maize). Gramene builds upon Ensembl and Reactome software, and is committed to open accesses and reproducible science based on the FAIR principles, providing both human and machine access to the data. Gramene provides integrated search capabilities and interactive views to visualize gene features, gene neighborhoods, phylogenetic trees, gene expression profiles, pathways, and cross-references. Powerful phylogenetic approaches, including protein-based gene trees with stable IDs and whole-genome DNA alignments, enable traversing between maize and other plant species. Gramene hosts curated rice pathways, and uses these curated pathways to generate orthology-based projections for other species. Maize data includes the hosting of the maize RefGen_V4 assembly including: i) functional descriptions for ~30K genes, ii) sub-genome designation and ohnologs, iii) transposable elements, and iv) V3-V4 gene ID conversion table, and assembly converter to lift over genomic coordinates between V2, V3, and V4. Variation data includes the Panzea's 2.7 GBS (~720K SNPs in 16,718 lines) and maize HapMap2 (~55 million SNPs in 104 lines) data sets. Visualizations of EBI Expression Atlas data are integrated into the search results panel, and both genome and pathway browsers. Other annotation tracks include methylome signatures, genome-wide long non-coding RNAs, and nascent transcriptomes.

Below is the full program for the Maize Tools & Resources Pre-MaizeMeeting Workshops, and the initation to the Gramene Workshop:

Schedule:

Dr. Tello-Ruiz will also present 2 Gramene related posters: "Mining Maize with Gramene" (workshop poster) and "Gramene maize pan-genome browser" (see abstract below).

Gramene maize pan-genome browser

Sharon Wei1, Joshua C Stein1, Andrew Olson1, Yinping Jiao1, Bo Wang1, Michael Campbell1, Marcela K. Tello-Ruiz1, Doreen Ware 1,2

1 Cold Spring Harbor Laboratory; Cold Spring Harbor, NY, USA 11724

2 USDA ARS NEA Plant, Soil & Nutrition Laboratory Research Unit; Ithaca, NY, USA 14853

Maize is the most genetically diverse crop in the world, with differences in gene content estimated between 5-20% among lines. Capturing the pan-Zea gene space and structural variation requires additional reference genomes, and the infrastructure to store, analyze and make  accessible. To support this effort, Gramene has developed a dedicated genus-level browser resource: maize-pangenome.gramene.org, built upon the Ensembl infrastructure and guided by FAIR practices.  Our first pass of this resource includes B73, W22, and PH207 complete reference genomes, along with  7 monocot and dicot outgroup species. These served as input to generate phylogenetic resources based on protein and whole-genome DNA alignments. Insights into ancestrally conserved regions and structural rearrangements are defined by pairwise whole-genome alignments and displayed in a number of informative ways, including a multi-species view that allows graphical stacking of browsers and interspecies navigation. The gene trees can be used to programmatically identify gene expansions and losses between different maize accessions, which may explain evolutionary adaptations, inaccuracies in the gene models, or errors in the underlying reference genome assemblies. We anticipate maize accessions like the NAM populations being added to this resource. To test the utility of these resource and to assess quality of the gene structure predictions, Gramene outreach efforts include the first maize annotation jamboree co-organized with the MaizeCODE project. This work constitutes an initial prototype to support the infrastructure to identify misannotated gene structures and a process to correct these guided by the gene trees. In addition to providing resources to support quality assessment, as well as insights into many outstanding questions in the evolutionary history of the Zea genus, this resource will provide a basis for functional characterization of genes and the identification of targets for agronomic improvement of maize. This project is funded by NSF (IOS-1127112) and partially from USDA-ARS (1907-21000-030-00D).