Collaborator: Brachypodium variation

Brachypodium sylvaticum variation


Following plant materials were used for generating the transcriptome sequences of B. sylvaticum.

    Species: Brachypodium sylvaticum (slender false-brome) NCBI Tax ID = 29664

    Genotypes/Populations: Seed materials are maintained by Prof. Mitch Cruzan from Department of Biology, Portland State University, Portland, Oregon USA. [-Cruzan lab].

    • Brasy-Gre: Greece (Population GRE, USDA accession PI 206546). A population from Avila
    • Brasy-Esp: Spain (Population SAV, USDA accession PI 318962)
    • Brasy-Cor: Corvallis, Oregon, USA (Population OR-C1)

    Source plant material: vascular leaf lamina from 60-week old plant. All plants were grown in a common greenhouse garden at Portland State University campus under 12 hours light at 25°C and 12 hours dark at 15°C.


  • NCBI-BioProject: [PRJNA182761]
  • NCBI-BioSample(s): [View samples]
  • Transcriptome Sequences (Illumina_reads): fastq files in gz zipped format [NCBI:SRA062855] - [get data]
  • Transcriptome Sequences (cDNA contigs and peptides): fasta format files - [get data]
  • Genome mapping (to Brachypodium distachyon Bd21 genome). Includes cDNA and SNP (GFF format files) - [get data]
  • Annotations (Gene Ontology and InterPro annotations) - [get data]
  • Phylogeny Analysis (SNP based phylogeny tree and alignment) - [get data]
  • RPKM (Gene expression data) - [get data]
  • SNP markers (GFF and VCF file formats) - [get data]
  • SSR markers - [get data]


Sequencing and De Novo Transcriptome Assembly of Brachypodium sylvaticum (Poaceae). Samuel E. Fox, Justin Preece, Jeffrey A. Kimbrel, Gina L. Marchini, Abigail Sage, Ken Youens-Clark, Mitchell B. Cruzan, and Pankaj Jaiswal. Applications in Plant Sciences 2013 1 (3), 1200011. [View Publication at]