Sequencing the Fusarium circinatum genome

 

Fusarium circinatum

Fusarium circinatum (teleomorph = Gibberella circinata) is the causal agent of pine pitch canker. Although the disease was first identified in the 1940s in North Carolina, the pathogen is now known to occur across the south eastern states and California in the United States, and in numerous countries worldwide including Haiti, Chile, Japan, Korea, Mexico, Italy, Spain and South Africa. The pitch canker fungus typically causes large resinous cankers on main trunks and lateral branches of susceptible pine trees, but can affect other plant parts as well (e.g., roots, shoots, female flowers and mature cones, and seed). The pathogen is also able to infect seedlings where it causes damping-off, shoot and tip die-back and mortality of established seedlings. Consequently, the disease is often associated significant economic losses due to reduced yields and tree mortality. For more information on pitch canker, F. circinatum and its affect on pine forestry, see the recent review published in 2008 in Australasian Plant Pathology, 37:319-334.

Genome Sequencing Project

For this project, we targeted an isolate of Fusarium circinatum (Fsp34) for which we have previously generated a genetic linkage map (see De Vos et al. 2007) and microsatellite-enriched genomic sequences (Santana et al. 2009). To determine the complete genome sequence for this isolate, nebulised total genomic DNA were sequenced with the Roche 454 GS-FLX Titanium platform at Inqaba Biotech (Pretoria, Gauteng, South Africa). To assist with the annotation procedure, EST libraries for this isolate were also prepared and sequenced using this pyrosequencing platform.

 

Gene-finding Jamboree 24-28 May 2010

 

The annotation of the F. circinatum genome was completed during a recently held Annotation Jamboree in Pretoria.The jamboree took place at FABI and among others utilized the computer laboratory of the University Bioinformatics Unit. During this event, annotators spent close to eight hours each day interrogating open reading frames (ORFs) generated from the MAKER genome annotation pipeline. The team of annotators included students and academic staff of the University of Pretoria and universities in the USA.


 

 

Pictures depicting the light and enthusiastic spirit that was characteristic throughout the Jamboree:

 

 

A) Mark Yandell. B) From left to right: Stephanie Slinski, Quentin Santana, Simon Martin, Oleg Reva, Stefan Bam. C) Irene Barnes and Osmond Mlonyeni. D) The annotators hard at work.

 

 

Group photo of the annotators with Mark Yandell:

Front row: Brenda Wingfield, Mmatshepho Phasha, Chrizelle Beukes, Kershney Naidoo.

2nd row: Irene Barnes, Rene Sutherland, Simon Martin, Stefan Bam.

3rd row: Emma Steenkamp, Gerda Fourie

4th row: Lieschen de Vos, Melissa Simpson, Oleg Reva.

5th row:Magriet van der Nest, Annie Chan, Albe van der Merwe.

6th Row: Fanus Venter, Alisa Postma, Martin Coetzee.

7th row: Markus Wilken, Quentin Santana, Renate Zipfel.

Back row: Stephanie Slinski, Mark Yandell, Darryll Herron.

 

Post jamboree meeting and wrap up session.

 

Important Fusarium Literature:

  • Wingfield MJ, Hammerbacher A, Ganley RJ, Steenkamp ET, Gordon TR, Wingfield BD, Coutinho TA, 2008. Pitch canker caused by Fusarium circinatum: A growing threat to pine plantations and forests worldwide. Australasian Plant Pathology 37,319-334.
  • De Vos L, Myburg AA, Wingfield MJ, Desjardins AE, Gordon TR, Wingfield BD, 2007. Complete genetic linkage maps from an interspecific cross between Fusarium circinatum and Fusarium subglutinans. Fungal Genetics and Biology 44, 701-714.

Funding

  • TPCP partners
  • NRF
 

 

 

 

 


 

FABI