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

Abstract

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.

Keywords: Plant Genetics and Genomics; abiotic stress; genome; perennial grass; transcriptome; transposable element.

Fig. 1.

Genome analysis and synteny. a) The total length of genomic features in 6 grass genomes. b) Syntenic relationships between B. sylvaticum and 5 other diploid grasses: B. distachyon, B. stacei, O. sativa, P. hallii, and S. bicolor.

Fig. 2.

Transcriptomic responses to cold stress. a) Venn diagram of up- and downregulated genes during cold to freezing and from freezing to recovery in crowns and leaves. The blue arrows indiate upregulated genes and the red arrows indicate downregulated genes. b) Heatmap of 9,475 significantly DEGs in at least 1 treatment.

Fig. 3.

Expression analysis using k-mean clustering approaches with normalized counts for 3,296 DEGs with variance >1.5 and mean expression >4 in the leaf and crown under cold, freezing, and recovery conditions.

Fig. 4.

Transcriptomic response to stress. a) The number of up- and downregulated genes at different timepoints under water deprivation, heat, and salt stresses. b) Venn diagram of up- and downregulated genes under water deprivation, heat, and salt stresses (combined timepoints for each treatment). c) Heatmap of 17,184 genes that were significantly differentially expressed genes in at least 1 timepoint and treatment.

Fig. 5.

Expression analysis using k-mean clustering approaches with normalized counts for the 1,911 DEGs with variance >1.5 and mean expression >4 in under heat, water deprivation (WD), and salt stress conditions.

Fig. 6.

Comparative genomics and phylostratigraphic analysis. a) Partial upset plot showing the number of orthologs shared by all 6 grasses, Brachypodium species, and species-specific orthologs. The full upset plot can be found in Supplementary Fig. 1. b) Phylostratigraphic map of B. sylvaticum. Numbers in parentheses denote the number of genes per phylostratum (PS1–PS13). Cell. org., cellular organisms described by PS1.