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

Authors: LEI, LI - Energy Joint Genome Institute; GORDON, SEAN - Energy Joint Genome Institute; LIU, LIFENG - Energy Joint Genome Institute; SADE, NIR - University Of California, Davis; LOVELL, JOHN - Hudsonalpha Institute For Biotechnology; RUBIO-WILHELMI, MARIA - University Of California, Davis; SINGAN, VASANTH - Energy Joint Genome Institute; SREEDASYAM, AVINASH - Hudsonalpha Institute For Biotechnology; HESTRIN, RACHEL - Energy Joint Genome Institute; PHILIPPS, JEREMY - Energy Joint Genome Institute; HERNANDEZ, BRIAN - Former ARS Employee; BARRY, KERRY - Energy Joint Genome Institute; SHU, SHENGQIANG - Energy Joint Genome Institute; JENKINS, JERRY - Hudsonalpha Institute For Biotechnology; SCHMUTZ, JEREMY - Hudsonalpha Institute For Biotechnology; GOODSTEIN, DAVID - Energy Joint Genome Institute; Thilmony, Roger; BLUMWALD, EDUARDO - University Of California, Davis; VOGEL, JOHN - Energy Joint Genome Institute

Submitted to: G3, Genes/Genomes/Genetics
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 9/28/2023
Publication Date: 10/26/2023
Citation: Lei, L., Gordon, S.P., Liu, L., Sade, N., Lovell, J., Rubio-Wilhelmi, M., Singan, V., Sreedasyam, A., Hestrin, R., Philipps, J., Hernandez, B.T., Barry, K., Shu, S., Jenkins, J., Schmutz, J., Goodstein, D., Thilmony, R.L., Blumwald, E., Vogel, J. 2023. The reference genome and abiotic stress responses of the model perennial grass Brachypodium sylvaticum. G3, Genes/Genomes/Genetics. https://doi.org/10.1093/g3journal/jkad245.
DOI: https://doi.org/10.1093/g3journal/jkad245

Interpretive Summary: Perennial grasses are important forage crops, emerging biomass crops, and have the potential to be more sustainable grain crops, but most are difficult experimental research subjects. Genomic resources, including a high-quality reference genome sequence and a abiotic-stress responsive gene expression atlas were created for the perennial model grass Brachypodium sylvaticum. These novel genomic and expression resources will be useful for the plant research community and will significantly advance research studying perennial grasses.

Technical Abstract: Perennial grasses are important forage crops, emerging biomass crops, and have the potential to be more sustainable grain crops. However, most perennial grass crops are difficult experimental subjects for reasons including 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 a perennial grass crop. Brachypodium sylvaticum has the potential to serve as such a model because its small size, rapid generation time, simple genetics, and transformability. Here we provide a fully assembled and annotated, high-quality Brachypodium sylvaticum genome. In addition, the global transcriptional responses of B. sylvaticum plants exposed to four abiotic stresses (water deprivation, heat, salt and freezing) are provided. Together, these results can be used to form testable hypotheses about how perennial grasses respond to stress and will allow B. sylvaticum to serve as a tractable perennial model system.