Gramene release 64 is out with 21 new reference genomes and the latest maize B73

The Gramene Knowledgebase Team is pleased to announce its Release #64 (see release notes) with the Genome browser providing access to information on 114 reference genomes and 123,064 gene family trees. This release features the new sequence assembly and gene annotation (version 5) of the B73 maize reference genome from Hufford et al (2021)*. We have also added 21 new reference genomes, including quinoa, asparagus, spelt, opium poppy, sesame, Persian walnut, a relative of wasabi, eucalyptus and white oak (roble) trees, nine varieties of bread wheat, and a variety of each, barley and potato. In addition, updates were applied to the assembly and annotation of the banana, white Guinea yam, and Peruvian cotton genomes. With these new and updated genomes, our comparative genomics collection totals 340 pairwise DNA alignments and 80 synteny maps. New SNP variation datasets are now provided for black and soy beans.

The Plant Reactome is the pathway knowledgebase of Gramene. We utilize the Reactome pathway data model to represent plant metabolic, transport and signaling pathways, developmental processes, organ differentiation, and transcriptional regulatory networks. Manual biocuration is conducted in Japonica rice, the reference species, and pathways are then projected via gene orthology to other species including crops and model plants, lower plants and single-cell photoautotrophs. In this release, homology-based pathway projections were added for version 5 of the B73 maize genome but version 4 pathway projections will continue to be available for comparison. Plant Reactome continues to host 320 rice curated pathways and their gene-orthology based projection for 106 species.

The Gramene Knowledgebase is a curated, open-source, integrated data resource for comparative functional genomics in crops and model plant species. The genome databases were built in direct collaboration with Ensembl Plants, and the Plant Reactome database was produced in collaboration with the Reactome project. Core funding for the project is provided by the Agricultural Research Service of the U.S. Department of Agriculture (USDA ARS 1907-21000-030-00D), and the National Science Foundation (NSF IOS-1127112). Please let us know if you have any questions or suggestions.

The Gramene Team

* To access the assembly and annotation of the 26 maize inbred lines that serve as the founders for the maize nested association mapping (NAM) population described in Hufford et al (2021), please see Gramene's Maize PanGenome site.