Improved protein-coding gene family trees available in Gramene's Oryza PanGenome release 3.1

Gramene's Oryza Pan-Genome (https://oryza.gramene.org) is a web portal for comparative plant genomics focused on rice varieties. In its release 3.1, the gene family trees were rebuilt using the same species included in release 3.0 with superior quality.

A total of 37,423 GeneTree families were constructed comprising 1,134,514 individual genes (1,187,461 input proteins). See updated stats here.

The new trees include the same species as the prior release 3.0: 25 Oryza genomes, Leersia perrieri (the most closely related species to the Oryza in the Oryzeae tribe), 6 plant outgroups (B73 maize, sorghum, Arabidopsis thaliana, grapevine, a vascular plant, and a single-celled green algae) and Drosophila, in order to allow comparisons between higher eukaryotes, lower plants, and the model Arabidopsis in the Oryza pan-genome.

For additional information, please see Oryza genome R3.1 release notes.

Core funding for the project was provided by the National Science Foundation (NSF IOS-1127112) and the Agricultural Research Service of the U.S. Department of Agriculture (USDA ARS 8062-21000-041-00D).