Brachypodium distachyon Bd21 Assembly & Annotation

Overview

Analysis Name Brachypodium distachyon Bd21 Assembly & Annotation
Sequencing technology ABI 3739
Assembly method ARACHNE v. 20071016_modified
Release Date 2018-01-24
Reference Publication(s)

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.

Abstract

Three 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

Assembly

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

Gene Predictions

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 Analysis

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

S genes

Summary

QueryChromosomeSize(bp)CoordinatestBLASTn HittBLASTn %IDDomain
DUF247II-SCM000881.35913057535944957-35946609LpSDUF247-II_chromosome176DUF247
HPS10-SCM000881.35913057535943205-35943338,
35943417-35943540
Ainsularis_HPS10-S243-
DUF247II-ZCM000884.32863013625885843-25886994LpZDUF247-II_chromosome252DUF247

Nucleotide

Protein

© 2023 National Genomics Data Center, China National Center for Bioinformation / Beijing Institute of Genomics, Chinese Academy of Sciences