Summary
Name
Whole Genome Assembly (v3.0) and Annotation (v3.2) of Brachypodium distachyon - cv. Bd21 (JGI)
Description

Assembly Improvement

This release represents the second improved Brachypodium distachyon (Bd21) genome including ~270 Mb of improved Brachypodium sequence. These regions were improved by dividing the gene space into ~2Mb overlapping pieces. Each region was manually inspected and then finished using a variety of technologies including Sanger (primer walks on subclones and fosmid templates, transposon sequencing on subclone templates), Illumina (small insert shatter libraries) and clone-based shotgun sequencing using both Sanger and Illumina libraries. 1,496 gaps were closed, and a total of 1.43 MB of base pairs was added to the assembly. Overall contiguity (contig N50) increased by a factor of 63 from 347.8Kb to 22 Mb.

Gene Prediction and Locus Naming

This v3.2 is GMI version of v3.1 both described below.

The v3.2 GMI annotation

Various Illumina RNA-seq reads were used to construct transcript assemblies using PERTRAN (Shu, unpublished pipeline) : ~1.6B pairs of geneAtlas, 96M pairs and ~1.9M 454. About 12M PacBio Iso-Seq CCSs were corrected and collapsed by genome guided correction pipleine (Shu, unpublished) to obtain 1.1M putative full length transcripts. 430,514 transcript assemblies were constructed using PASA (Haas, 2003) from RNA-seq transcript assemblies, clustered CCSs above, and ESTs. Gene models of v3.1 on assembly v3.0 were used as a start point in GMI.

Program, Pipeline, Workflow or Method Name
Phytozome
Program Version
v3.1
Algorithm
Date Performed
Monday, February 13, 2023
Data Source
Source Name
: Phyzotome
Source Version
: 13.0
Source URI
: https://phytozome-next.jgi.doe.gov/info/Bdistachyon_v3_2
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