Zymoseptoria tritici (MG2)

Zymoseptoria tritici Assembly and Gene Annotation

About Zymoseptoria tritici

Zymoseptoria tritici (formely known as Mycosphaerella graminicola) causes septoria tritici blotch in wheat, the second most important disease in the United States after rust. This disease is heavily targeted by the fungicide companies worldwide being nevertheless very difficult to control.


The latest version of the Zymoseptoria tritici genome assembly was released in September 2008. The genome comprises 21 chromosomes with a total size of 39.7 Mb and encodes about 10952 protein-coding genes.


The genome sequence, assembly and protein coding genes annotation of the Zymoseptoria tritici genome have been generated by the JGI under funding of the US Department of Energy's Office of Science, Biological and Environmental Research Program, and by the University of California, Lawrence Berkeley National Laboratory.

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.

Expression studies

Transcriptome data for Zymoseptoria tritici IPO323 produced by Charlie Cairns and Ken Haynes at the University of Exeter (BBSRC grant number BB/I025956/1) is also available for viewing in the browser as BAM tracks.


We constructed a variation database using the resequencing data of Zymoseptoria tritici. Sequence read data for the study SRP017760 was downloaded from ENA Short Read Archive and mapped against the Z.tritici genome using Burrows-Wheeler Alignment Tool (Li H.and Durbin R.Bioinformatics 2010) and variation calling was done using SAMtools (Li H.et.al Bioinfomratics 2009).


  1. Analysis of expressed sequence tags from the wheat leaf blotch pathogen Mycosphaerella graminicola (anamorph Septoria tritici).
    Keon J, Antoniw J, Rudd J, Skinner W, Hargreaves J, Hammond-Kosack K. 2005. Fungal Genet. Biol.. 42:376-389.
  2. Finished genome of the fungal wheat pathogen Mycosphaerella graminicola reveals dispensome structure, chromosome plasticity, and stealth pathogenesis.
    Goodwin SB, M'barek SB, Dhillon B, Wittenberg AH, Crane CF, Hane JK, Foster AJ, Van der Lee TA, Grimwood J, Aerts A et al. 2011. PLoS Genet.. 7:e1002070.

Picture credit: Picture credit: Rothamsted Bioimaging Dept, Copyright Rothamsted Research Ltd.

Other Data

Gene models reannotated by Rothamsted Research using MAKER Annotation software are now available to view in the genome browser, under the track name "ZtRRes v1.0 Genes". In addition, ESTs downloaded from dbEST have been aligned to the genome using exonerate.

More information

General information about this species can be found in Wikipedia.



AssemblyMG2, INSDC Assembly GCA_000219625.1, Sep 2008
Database version112.2
Golden Path Length39,686,251
Genebuild byJGI
Genebuild methodImport
Data sourceJGI

Gene counts

Coding genes10,933
Non coding genes147
Small non coding genes147
Gene transcripts11,091


Short Variants508,257