Analysis Name | Brachypodium distachyon Bd21 Assembly & Annotation |
Sequencing technology | ABI 3739 |
Assembly method | ARACHNE v. 20071016_modified |
Release Date | 2018-01-24 |
International Brachypodium Initiative. Genome sequencing and analysis of the model grass Brachypodium distachyon. Nature. 2010 Feb 11;463(7282):763-8. doi: 10.1038/nature08747.
AbstractThree subfamilies of grasses, the Ehrhartoideae, Panicoideae and Pooideae, provide the bulk of human nutrition and are poised to become major sources of renewable energy. Here we describe the genome sequence of the wild grass Brachypodium distachyon (Brachypodium), which is, to our knowledge, the first member of the Pooideae subfamily to be sequenced. Comparison of the Brachypodium, rice and sorghum genomes shows a precise history of genome evolution across a broad diversity of the grasses, and establishes a template for analysis of the large genomes of economically important pooid grasses such as wheat. The high-quality genome sequence, coupled with ease of cultivation and transformation, small size and rapid life cycle, will help Brachypodium reach its potential as an important model system for developing new energy and food crops.
Assembly statistics
Genome size | 271.2 Mb |
Number of chromosomes | 5 |
Number of scaffolds | 14 |
Scaffold N50 | 30.2 Mb |
Scaffold L50 | 4 |
Number of contigs | 35 |
Contig N50 | 22 Mb |
Contig L50 | 5 |
Assembly level | Chromosome |
The Brachypodium distachyon Bd21 Assembly file is available in FASTA format.
Downloads
Chromosomes (FASTA file) | GCA_000005505.4_Brachypodium_distachyon_v3.0_genomic.fna.gz |
The Brachypodium distachyon Bd21 genome gene prediction files are available in GFF3 and FASTA format.
Downloads
Genes (GFF3 file) | GCA_000005505.4_Brachypodium_distachyon_v3.0_genomic.gff.gz |
CDS sequences (FASTA file) | GCA_000005505.4_Brachypodium_distachyon_v3.0_cds_from_genomic.fna.gz |
Protein sequences (FASTA file) | GCA_000005505.4_Brachypodium_distachyon_v3.0_protein.faa.gz |
Functional annotation for the Brachypodium distachyon Bd21 is available for download below. The proteins were analyzed using InterProScan to assign InterPro domains(Pfam).
Downloads
Domain from InterProScan | Brachypodium_distachyon.Pfam.tsv.gz |
Summary
Query | Chromosome | Size(bp) | Coordinates | tBLASTn Hit | tBLASTn %ID | Domain |
DUF247II-S | CM000881.3 | 59130575 | 35944957-35946609 | LpSDUF247-II_chromosome1 | 76 | DUF247 |
HPS10-S | CM000881.3 | 59130575 | 35943205-35943338,35943417-35943540 | Ainsularis_HPS10-S2 | 43 | - |
DUF247II-Z | CM000884.3 | 28630136 | 25885843-25886994 | LpZDUF247-II_chromosome2 | 52 | DUF247 |
Nucleotide
Protein