Gramene Oryza PanGenome is released with 15 new rice genomes

Submitted by marcela.karey on Tue, 10/19/2021 - 21:00

Oryza PanGenome Release 3.0

Released: October 2021

Gramene's Oryza Pan-Genome (https://oryza.gramene.org) is a web portal for comparative plant genomics focused on rice varieties. In its third release, the Oryza pan-genome provides access to 15 new rice genomes: 9 indica, 2 aus, and 4 japonica varieties, including Carolina Gold rice (Zhou et al, 2020; Wang et al, 2018; Stein et al, 2018), and one updated reference genome: Oryza sativa indica (var. 93-11). These 16 Oryza genomes were added to the collection of 10 Oryza genomes in Gramene to a total of 25 Oryza genomes.

Fifteen new Oryza genomes:

One updated Oryza genome: 

Together with 6 plant outgroup species (Arabidopsis thaliana, sorghum, grapevine, Chlamydomonas, Selaginella, and 2 assembly versions of maize: v4 and v5), the 25 Oryza genomes and Leersia perrieri were used to build 37,315 protein-coding gene family trees. These family trees were constructed with 1,184,741 input proteins from 1,131,828 individual genes.

Baseline gene expression for the Japonica reference is available via the Oryza Pan-Genome search interface and linked to the Expression Atlas, while differential gene expression for the same species is only available on the Expression Atlas website.

For the 9 Oryza genomes in the prior release of the Pan-Genome (i.e., O. sativa japonica, O. barthii, O. brachyantha, O. glaberrima, O. glumaepatula, O. meridionalis, O. nivara, O. punctata, and O. rufipogon), as well as for L. perrieri and the other outgroups, orthology-based pathway projections are available via the Oryza Pan-Genome search interface. Similarly for those genomes, complementary pairwise DNA alignments (e.g., 81 for O. sativa Japonica) and/or synteny maps (e.g., 19 for O. sativa Japonica) are available on the Gramene website. Gramene continues to host genetic variation totalling over 40 million SNPs for the Japonica reference, O. glaberrima and O. glumaepatula.

The genome databases were built in direct collaboration with the Gramene and Ensembl Plants projects. Gene expression and pathway associations were facilitated through collaboration with the Expression Atlas and Plant Reactome projects, respectively. 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) to the Ware Lab at the Cold Spring Harbor Laboratory.

For aditional details, please see the release notes (LINK) at the Gramene Oryza Pan-Genome site.

 

References:

Stein, Joshua C., Yeisoo Yu, Dario Copetti, Derrick J. Zwickl, Li Zhang, Chengjun Zhang, Kapeel Chougule, et al. 2018. “Genomes of 13 Domesticated and Wild Rice Relatives Highlight Genetic Conservation, Turnover and Innovation across the Genus Oryza.” Nature Genetics 50 (2): 285–96.

Wang, Wensheng, Ramil Mauleon, Zhiqiang Hu, Dmytro Chebotarov, Shuaishuai Tai, Zhichao Wu, Min Li, et al. 2018. “Genomic Variation in 3,010 Diverse Accessions of Asian Cultivated Rice.” Nature 557 (7703): 43–49.

Zhou, Yong, Dmytro Chebotarov, Dave Kudrna, Victor Llaca, Seunghee Lee, Shanmugam Rajasekar, Nahed Mohammed, et al. 2020. “A Platinum Standard Pan-Genome Resource That Represents the Population Structure of Asian Rice.” Scientific Data 7 (1): 113.