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

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 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 Brachypodium sylvaticum, an essential resource for a modern model system. In addition, we conducted transcriptomic studies under four abiotic stresses (water, heat, salt, 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.

Reductional dysploidy and genome size diversity in Pooideae, the largest subfamily of grasses (Poaceae)

“…data). Therefore, autopolyploidy seems likely in this case, which is supported by the largely concordant 1Cx values of 0.35-0.40 pg and the MC of 0.07-0.08 pg of the widespread diploid and the new tetraploid cytotype of B. distachyon s.s.Two perennial species of Brachypodium were additionally sampled, namely two accessions of B. , the sequenced genome was found to be 717 Mbp (≈ 0.73 pg/2C)(Lei et al 2024), which is therefore compatible with the FCM estimates. The 1Cx value in B. sylvaticum was 0.52 pg and the MC was 0.06 pg, while these values cannot be calculated for the allopolyploid B. pinnatum.…”

“…2024: Table2), which makes them similar to the tribe Brachypodieae with also 'miniaturized genomes' with rather few repetitive DNA in their genomes. This is shown by the average of only 36 Mbp of repetitive DNA present in the entire 375 Mbp rice genome (3,010 accessions of Oryza sativa analyzed) and 42 Mbp in the 234 Mbp genome of Brachypodium stacei, respectively(Wang et al, 2018;Lei et al, 2024). These very small amounts of repetitive DNA compared to other grasses may represent an evolutionarily 'derived' feature of their genomes rather than an ancestral trait.…”

Expansions and contractions of repetitive DNA elements reveal contrasting evolutionary responses to the polyploid genome shock hypothesis in Brachypodium model grasses

“…The cool seasonal genus Brachypodium , consisting of approximately 23 taxa ( Catalan et al., 2016 ; Catalán et al., 2023 ), has been selected as a model functional system for cereal and biofuel crops and to investigate the evolution of polyploidy in grasses. Annotated reference genomes and considerable genomic resources have been produced for its three annual species ( B. distachyon, B. stacei, B. hybridum ) ( Scholthof et al., 2018 ; Hasterok et al., 2022 ; Mu et al., 2023a , b ; Chen et al., 2024 ) and for the slender perennial B. sylvaticum ( Lei et al., 2024 ). Comparative genomic studies of the annual species evidenced that the allotetraploid B. hybridum of recurrent origin did not undergo significant genomic restructuring, showing equivalently inherited parental transposon contents in its two subgenomes ( Gordon et al., 2020 ; Scarlett et al., 2023 ; Mu et al., 2023a ).…”