Genomics Resource for Brachypodium sylvaticum

About Brachypodium sylvaticum

Brachypodium sylvaticum also called slender false-brome is a perennial bunchgrass native to Europe, Asia, and North Africa. It is a close relative of Brachypodium distachyon which is a model plant species for bioenergy feedstock. In much of the United States, B. sylvaticum is considered an invasive species and is listed as a noxious weed covering the west coast of California, Oregon, and Washington. For more information on the species and how to identify the plant please visit the respective webpages on the King County, Oregon Department of Agriculture and the Institute of Applied Ecology websites.

PLANT MATERIAL

Following plant materials were used for generating the transcriptome sequences of B. sylvaticum. View NCBI-BioProject [PRJNA182761]

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].

• NCBI-BioSample(s): [View samples]
• 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
• Plant Ontology (Anatomy) : leaf lamina (PO:0020039); vascular leaf PO:0009025)
• Plant Ontology (growth stages): leaf production stage (PO:0007133)
Growth condition: 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.
• Plant Environment Ontology: green house study (EO:0007248); intermittent light regimen (EO:0007128)

DATA SETS

From Jaiswal lab

• 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]
• SNPs (GFF and VCF file formats) - [get data]
• SSRs - [get data]

Browse data from external sources

• Browse at Gramene's Brachypodium distachyon genome browser. Users need to configure and select the data tracks to visualize
• From Brachypodium.org
• BAC libraries [-Visit publication]
• NCBI-ENTREZ [-Browse]

Publication Citation

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 http://www.bioone.org/doi/abs/10.3732/apps.1200011]

OTHER PUBLICATIONS

Pubmed - [browse]
Google Scholar - [browse]

Note: B. sylvaticum flower image source (King County Website)