Fusarium oxysporum Assembly and Gene Annotation

About the Fusarium oxysporum f.sp. lycopersici genome

Fusarium oxysporum comprises a group of soil inhabitants that can exist as saprophytes in the soil debris but also as pervasive plant endophytes colonizing the plant roots. Many strains of these species are pathogenic to plant crops. One of these strains, Fusarium oxysporum f.sp. lycopersici, is the causal agent of fusarium wilt in tomatoes. The first symptoms of the plant are yellowing and weakness in one side of the plant and progress with wilting of the leaves and browning of the vascular system leading eventually to leaf death and inhability to produce fruits.

The genome sequence, assembly and protein coding genes annotation of the Fusarium oxysporum f.sp. lycopersici (4287) genome have been generated by the Broad Institute as part of their work on the Fusarium Comparative Sequencing Project. The genome has been sequenced to a coverage of 6x and has a total estimated size of 59.9 Mb represented in 114 scaffolds.

Variation Data

Fusarium oxysporum exhibits genetic plasticity which makes it a destructive pathogen across a wide range of crops. We constructed a variation database comparing 27 different strains of this species. Sequence read data was downloaded from ENA Short Read Archive and mapped against the Fusarium oxysporum f.sp. lycopersici 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).

References

1. Comparative genomics reveals mobile pathogenicity chromosomes in Fusarium.
   Ma LJ, van der Does HC, Borkovich KA, Coleman JJ, Daboussi MJ, Di Pietro A, Dufresne M, Freitag M, Grabherr M, Henrissat B et al. 2010. Nature. 464:367-373.
2. Identification of genes up-regulated during conidiation of Fusarium oxysporum through expressed sequence tag analysis.
   Iida Y, Ohara T, Tsuge T. 2006. Fungal Genet. Biol.. 43:179-189.

Picture credit: Picture credit: Keith Weller

Other Data

• 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.
• 'Expressed Sequence Tags' (ESTs) from dbEST are aligned to the genome using Exonerate.

More information

General information about this species can be found in Wikipedia.