Whole Genome Assembly (v2.0) and Annotation (v2.2) of Setaria italica - cv. Yugu1 (JGI)


Setaria italica cv. Yugu1 was sequenced and assembled by the Joint Genome Institute (JGI) in collaboration with community researchers. Sanger sequencing was performed on whole-genome shotgun clone libraries having different insert sizes. Reads totalling 8.29x coverage were assembled with Arachne giving scaffolds that were arranged predominantly into nine pseudomolecules.


Protein-coding genes were predicted using the standard JGI plant gene annotation pipeline. They used ESTs and homologous peptides from Arabidopsis, Brachypodium, rice and sorghum, mapped with BLAT alignments of PASA and EXONERATE, with GenomeScan, FGENESH+ and FGENESH_EST. BACs and fosmids were annotated using AUGUSTUS with maize parameters to predict gene models, which were compared to GenBank, TAIR and IRGSP/RAP proteins and manually inspected. Gene models were validated with RNA-seq data.

Source : Phytozome

Program, Pipeline, Workflow or Method Name
Assembly & annotation, performed by JGI
Program Version
v 2.2
Date Performed
Sunday, January 13, 2019
Data Source
Source Name
: JGI-Phytozome Setaria italica assembly/annotation
Source Version
: v2.2 [312]
Source URI
Bennetzen JL, Schmutz J, Wang H, Percifield R, Hawkins J, Pontaroli AC, Estep M, Feng L, Vaughn JN, Grimwood J, Jenkins J, Barry K, Lindquist E, Hellsten U, Deshpande S, Wang X, Wu X, Mitros T, Triplett J, Yang X, Ye CY, Mauro-Herrera M, Wang L, Li P, Sharma M, Sharma R, Ronald PC, Panaud O, Kellogg EA, Brutnell TP, Doust AN, Tuskan GA, Rokhsar D, Devos KM. Reference genome sequence of the model plant Setaria.. Nature biotechnology. 2012 May 13; 30(6):555-61.
This record has the following annotations.
There are no annotations of this type
There are 0 relationships.
There are no relationships
Loading content