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

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

doi:10.1093/g3journal/jkad245

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

Journal Article · 26 October 2023 · G3

DOI: https://doi.org/10.1093/g3journal/jkad245 · OSTI ID:2267598

^[1]; Gordon, Sean P. ^[1]; Liu, Lifeng ^[1];

^[2];

^[3]; Rubio Wilhelmi, Maria Mar ^[4]; Singan, Vasanth ^[1];

^[5]; Hestrin, Rachel ^[1]; Phillips, Jeremy ^[1]; Hernandez, Bryan T. ^[6]; Barry, Kerrie ^[1];

^[1];

^[5];

^[3]; Goodstein, David M. ^[1];

^[6];

^[4];

^[1]

USDOE Joint Genome Institute (JGI), Berkeley, CA (United States)
Univ. of California, Davis, CA (United States); Tel Aviv Univ., Tel Aviv (Israel)
USDOE Joint Genome Institute (JGI), Berkeley, CA (United States); HudsonAlpha Institute for Biotechnology, Huntsville, AL (United States)
Univ. of California, Davis, CA (United States)
HudsonAlpha Institute for Biotechnology, Huntsville, AL (United States)
USDA‐ARS, Albany, CA (United States). Western Regional Research Laboratory

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.

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Research Organization:: Lawrence Berkeley National Laboratory (LBNL), Berkeley, CA (United States)

Sponsoring Organization:: USDOE Office of Science (SC), Biological and Environmental Research (BER); USDOE Joint Genome Institute (JGI)

Grant/Contract Number:: AC02-05CH11231; SC0001526; SC0008797

OSTI ID:: 2267598

Alternate ID(s):: OSTI ID: 2229004; OSTI ID: 2439381

Journal Information:: G3, Vol. 14, Issue 1; ISSN 2160-1836

Publisher:: Genetics Society of AmericaCopyright Statement

Country of Publication:: United States

Language:: English

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59 BASIC BIOLOGICAL SCIENCES
genome
perennial grass
transcriptome
abiotic stress
transposable element
plant genetics and genomics

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

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References (90)

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