The reference genome and abiotic stress responses of the model perennial grass Brachypodium sylvaticum

Li Lei, Sean P. Gordon, Lifeng Liu, Nir Sade, John T. Lovell, Maria Del Mar Rubio Wilhelmi, Vasanth Singan, Avinash Sreedasyam, Rachel Hestrin, Jeremy Phillips, Bryan T. Hernandez, Kerrie Barry, Shengqiang Shu, Jerry Jenkins, Jeremy Schmutz, David M. Goodstein, Roger Thilmony, Eduardo Blumwald, John P. Vogel*

*Corresponding author for this work

Research output: Contribution to journalArticlepeer-review


Perennial grasses are important forage crops and emerging biomass crops and have the potential to be more sustainable grain crops. However, most perennial grass crops are difficult experimental subjects due to their large size, difficult genetics, and/or their recalcitrance to transformation. Thus, a tractable model perennial grass could be used to rapidly make discoveries that can be translated to perennial grass crops. Brachypodium sylvaticum has the potential to serve as such a model because of its small size, rapid generation time, simple genetics, and transformability. Here, we provide a high-quality genome assembly and annotation for B. sylvaticum, an essential resource for a modern model system. In addition, we conducted transcriptomic studies under 4 abiotic stresses (water, heat, salt, and freezing). Our results indicate that crowns are more responsive to freezing than leaves which may help them overwinter. We observed extensive transcriptional responses with varying temporal dynamics to all abiotic stresses, including classic heat-responsive genes. These results can be used to form testable hypotheses about how perennial grasses respond to these stresses. Taken together, these results will allow B. sylvaticum to serve as a truly tractable perennial model system.

Original languageEnglish
Article numberjkad245
JournalG3: Genes, Genomes, Genetics
Issue number1
StatePublished - Jan 2024


FundersFunder number
U.S. Department of Energy Joint Genome Institute
U.S. Department of EnergyDE-AC02-05CH11231, DE-SC0001526, DE-SC0008797
Office of Science
Biological and Environmental Research


    • Plant Genetics and Genomics
    • abiotic stress
    • genome
    • perennial grass
    • transcriptome
    • transposable element


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