Puccinia graminis Ug99 (v1)

Puccinia graminis Ug99 Assembly and Gene Annotation

The inclusion of the Puccinia graminis f. sp. tritici genome in Ensembl Genomes has been funded by the award of a grant from the Bill & Melinda Gates Foundation to EBI, the Broad Institute, and the USDA-ARS Cereal Disease Laboratory.

Puccinia graminis is an obligate plant pathogen, and the causal agent of stem rust, serious disease in cereal crops. An epidemic of stem rust on wheat caused by race TTKSK (sampled in the reference isolate Ug99) is currently spreading across Africa, Asia and the Middle East and is causing major concern due to the large numbers of people in these areas dependent on wheat for sustenance. Puccinia graminis Ug99 isolate has a unique virulence profile that can overcome many key wheat rust resistance genes and is spreading rapidly. Rust pathogens change rapidly, often by mutation, resulting in six additional variants now recognized in the Ug99 lineage.

The sequencing, assembly and annotation of protein coding genes from the Puccinia graminis (Ug99) genome has been generated by the Broad Institute as part of their work on the Puccinia group of fungi.

Non coding RNA genes have been annotated using tRNAScan-SE (Lowe, T.M. and Eddy, S.R. 1997), RFAM (Griffiths-Jones et al 2005), and RNAmmer (Lagesen K.,et al 2007); additional analysis tools have also been applied.

A variation database has been constructed by comparing this genome with Puccinia graminis f. sp. tritici sequence read data (study PRJNA253722). Reads were mapped against the Puccinia graminis Ug99 genome using BWA (Li H.and Durbin R.Bioinformatics 2010) and variations called using SAMtools (Li H.et.al Bioinformatics 2009).

More information

General information about this species can be found in Wikipedia.



Assemblyv1, Apr 2014
Database version104.1
Golden Path Length118,341,764
Genebuild byBroad
Genebuild methodImport
Data sourceBroad Institute

Gene counts

Coding genes22,154
Non coding genes3,072
Small non coding genes3,072
Gene transcripts27,682


Short Variants1,319,719

About this species