Gramene book chapter in the Plant Bioinformatics volume of the Methods in Molecular Biology protocols series

In recent months, the Plant Bioinformatics volume of the Methods in Molecular Biology protocols series edited by Professor David Edwards of the University of Queensland, Australia, was published.  This volume included 18 chapters covering various topics of interest to the plant research community and featured bioinformatic resources available for plant researchers.  The Gramene Database was featured in one of those chapters.

The Gramene chapter was the first publication describing Gramene’s new web interface, which was intended to provide a simplified portal to a vast set of plant genome and pathway annotations. The resource itself is an integrated informatics platform for accessing, visualizing, and comparing plant genomes and biological pathways.  Although it was originally conceived to target grasses, Gramene grew to host annotations for economically important and research model crops, including wheat, potato, tomato, banana, grape, poplar, and Chlamydomonas.  If offers a comparative platform that leverages a phylogenetic framework for genome comparison and the use of ontologies to integrate structural and functional annotation data.

The Gramene chapter outlines in detail system requirements for our users and database hosting, data types and basic navigation within Gramene, and provides protocols with examples for how to:

1. View a phylogenetic tree for a family of transcription factors
2. Explore genetic variation in the orthologues of a gene with a known trait association
3. Upload, visualize, and privately share end user data into a new genome browser track

The examples and data content correspond to Gramene data build 41 which was released to the public in May 2014, and only included 33 complete reference genomes and 7 partial (chromosme 3s) genomes.  To date, 3 of those partial genomes have been fully sequenced, and 3 more new assemblies were added to Gramene's reference assembly collection, making a total of 39 fully sequenced plant genomes since September of 2014.  Several assemblies and their corresponding gene annotations have also undergone significant updates, especially the new bread wheat (Triticum aestivum) assembly, since the publication of this volume.  Genetic and/or structural variation also grew from 8 to 11 species.  Since build 41, the Plant Reactome also grew from only hosting a handful of curated rice reference pathways and orthology-based projections of rice pathways to Arabidopsis thaliana and Zea mays, to currently host over 200 curated rice reference pathways and orthology-based projections for 58 species, including Arabidopsis and maize.  The richness of this chapter lies in the step-by-step walk-through procotols responding to the 3 common queries listed above.  We encourage readers to get a copy of this book and get familiar with the publicly available online resources and common protocols in use today for plant research.

In addition to a chapter about Gramene, the Plant Bioinformatics volume included 17 additional chapters covering subjects of interest to the plant research community that include related online plant resources like Ensembl Plants by Bolser et al, MaizeGDB by Harper et al, WheatGenome.info by Lai, BRAD (Brassica Database) by Wang et al, and the Plant Ontology by Cooper and Jaiswal.  It also included chapters describing more generic resources like GenBank by Sayers and Karsch-Mizrachi, UniProtKB/Swiss-Prot by Boutet et al, and KEGG by Kanehisa; compilations of resoures like a chapter on Plant Pathway Databases by Jaiswal and Usadel, and a description on Plant Resources at the PGSB/MIPS by Spannagl et al; and several chapters describing specific methodologies for example to align short reads, identify genomic regions, find and characterize repeats, visualize Next Generation Sequencing assemblies and mappings, analyze RNA-Seq data, and analyze Genotyping-By-Sequencing data.